OTTAWA - Fear may be escalating over the influence of al Qaeda and other Islamist fighters among Syria's rebels, but Canada's foreign affairs minister says he's more concerned about the fate of the country's religious minorities.

John Baird offered that counterpoint this past week on a growing area of concern in the Syria conflict: whether the radical jihadists among the rebels fighting to overthrow Syrian President Bashar Assad pose a long-term threat to the country.

Many analysts question whether a repeat of Iraq, Afghanistan or Somalia could be in store if jihadist elements gain strength in the anti-Assad uprising that has left 20,000 dead since March 2011. The foreign minister of Indonesia shared that view this week on a visit to Ottawa.

"Some extremists from the region have made their way in. I believe they are a minority of those fighting Assad's repression," said Baird, who travelled to neighbouring Jordan and Syria last month.

"Our concern is not so much Islamist groups. It's anyone who has radical or extreme views. There is not a single opposition in Syria. There are oppositions."

The bigger problem in Baird's view is that "civility and harmony" within Syria's various groups — Alawites, Christians, Kurds, Shiia and Sunni Muslims — could be undermined if the country fractures.

"What we don't want to see (is) anyone singled out for retribution, retaliation, particularly the ethnic minorities in the country," he said. "A number of us have a significant fear in that regard."

It's a position that's in keeping with the government's foreign policy focus on protecting the rights of religious minorities. Baird has yet to formally announce the long-promised Office of Religious Freedom within his department, but that hasn't stopped the minister from regularly highlighting the issue.

Indonesian Foreign Minister Marty Natalegawa said he believes the conditions on the ground in Syria are conducive to the rise of extremist groups in Syria.

"If you have a condition of anarchy, however it is brought about in the first place, whether it's the Syrian situation or previously Iraq, Afghanistan, of course the classic case, in Somalia … it tends to create conditions conducive," Natalegawa told The Canadian Press prior to his meeting with Baird in Ottawa.

"That is why we have to quickly bring about an end of the conflict in Syria, setting aside the political question of who is coming and who is going."

Natalegawa bases that opinion on Indonesia's own hard struggle with terrorism within its own borders.

The South Asian country is home to the world's largest Muslim population. Since the 9-11 attacks it has worked hard to clamp down on al Qaeda affiliated groups within its sprawling borders, spread over a vast archipelago. Indonesia was rocked by the bombing of a Bali nightclub in 2002 and a series of hotel bombings in its capital, Jakarta, in 2009.

Natalegawa said he planned to share his views on Syria with Baird in their meeting, which was mainly focused on boosting trade between the two countries.

As the two foreign ministers sat down in Ottawa, yet another analysis emerged that warned the West against turning a blind eye towards the influence of jihadists in the Syrian rebel forces.

"Our collective excitement at the possibility that the Assad regime will be destroyed, and the Iranian ayatollahs weakened in the process, is blurring our vision and preventing us from seeing the rise of al Qaeda in the region," wrote Ed Husain, a Middle East expert with the U.S.-based Council on Foreign Relations, in the National Review Online.

Husain said it is not credible for the West to ask the Syrian rebels to "jettison" foreign jihadists when it won't intervene militarily to stop the bloodshed.

The continued presence of jihadist fighters raises serious questions about the safety of the Syria's stockpile of chemical and biological weapons if the Assad regime falls, said Fen Hampson, director of Global Security of the Waterloo, Ont. Centre for International Governance Innovation.

"That's a big worry. They don't have to stay in Syria. As people get their hands on them, they can be smuggled and used elsewhere," he said.

Earlier this week, President Barack Obama raised the stakes in the conflict when he said the U.S. might have to intervene if chemical weapons were used or moved. He warned of rebel fighters or militants on either side of civil war getting their hands on the stockpile.

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  • Jordanian Foriegn Minister Nasser Judeh and his Canadian counterpart John Baird, right, visit the Zaatari camp for Syrian refugees in Mafraq, Jordan, Saturday, Aug. 11, 2012. (AP photo/Mohammad Hannon)

  • Canadian Foreign Affairs Minister John Baird greets a Syrian refugee boy s at Zaatari refugee camp, in Mafraq, Jordan, Saturday, Aug. 11, 2012. (AP photo/Mohammad Hannon)

  • Canadian Foreign Affairs Minister John Baird, center, stops by UNICEF classroom tent during his tour at Zaatari camp for Syrian refugees in Mafraq, Jordan, Saturday, Aug. 11, 2012. (AP photo/Mohammad Hannon)

  • Jordanian Foriegn Minister Nasser Judeh , center and his Canadian counterpart John Baird, right,visit Zaatari camp for Syrian refugees in Mafraq, Jordan, Saturday, Aug. 11, 2012. (AP photo/Mohammad Hannon)

  • Canadian Foreign Affairs Minister John Baird, speaks to one of the Syrian refugees at Zaatari refugee camp with his Jordanian counterpart Nasser Judeh, right,, in Mafraq, Jordan, Saturday, Aug. 11, 2012. (AP photo/Mohammad Hannon)


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lebanon Hussein Ali Omar, 60, one of 11 Lebanese Shiite pilgrims that Syrian rebels have been holding for three months in Syria, hugs his mother, right, upon arrival at his house in the southern suburb of Beirut, Lebanon, 2012. Syrian rebels freed Omar on Saturday in a move aimed at easing cross-border tensions after a wave of abductions of Syrian citizens in Lebanon. The Shiite pilgrims were abducted May 22 after crossing into Syria from Turkey on their way to Lebanon. (AP Photo/Hussein Malla)


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France24 correspondents Matthieu Mabin and Sofia Amara report from the front lines of a rebel offensive against the Syrian army in Damascus.

Watch the exclusive report in the video below.

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syria This image made from video and released by Shaam News Network and accessed Thursday, Aug. 23, 2012, purports to show the funeral of children in Daraya, near Damascus, Syria. Syrian troops backed by tanks and helicopters broke into a Damascus suburb on Thursday following two days of shelling and intense clashes as part of a widening offensive by President Bashar Assad's forces to seize control of parts of the capital and surrounding areas from rebel fighters, activists said. At least 15 people were killed in the offensive on Daraya, only a few miles (kilometers) southwest of Damascus. (AP Photo/Shaam News Network SNN via AP video)


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Clashes between Assad supporters and opponents of the Syrian regime killed two people in Lebanon on Friday, the Associated Press reports. 17 people were injured.

The AP gives more context:

Syria was in virtual control of its smaller neighbor for many years, posting tens of thousands of troops in Lebanon, before withdrawing under pressure in 2005. Even without soldiers on the ground, Syria remains influential, and its civil war has stirred longstanding tensions that have lain under Lebanon's surface.

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lebanon A Sunni gunman fires a gun during clashes that erupted between pro and anti-Syrian regime gunmen in the northern port city of Tripoli, Lebanon, Friday, Aug. 24, 2012. The latest round of fighting first erupted on Monday in northern Lebanon and at least 15 have been killed in Tripoli this week and more than 100 have been wounded in fighting that is a spillover from Syria's civil war. (AP Photo/Hussein Malla)


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syria Syrian boy Musataf Alhafiz, 11, who fled his home with his family due to fighting between the Syrian army and the rebels, carries his brother Saif, 9 months, while he and others take refuge at the Bab Al-Salameh border crossing, in hopes of entering one of the refugee camps in Turkey, near the Syrian town of Azaz, Thursday, Aug. 23, 2012. Thousands of Syrians who have been displaced by the country's civil war are struggling to find safe shelter while shelling and airstrikes by government forces continue. (AP Photo/Muhammed Muheisen)


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Helicopter gunships shelled Damascus on Wednesday as Syrian security forces intensified their assault on the capital. Activists report that at least 47 people were killed.

"The whole of Damascus is shaking with the sound of shelling," a woman in the neighborhood of Kfar Souseh told Reuters.

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lebanon Lebanese commandos ride in an armored personnel carrier in preparation to enter the area of clashes between supporters and opponents of the Syrian regime, in the northern port city of Tripoli, Lebanon, Wednesday, Aug. 22, 2012. The civil war in Syria is affecting its fragile, tiny neighbor Lebanon in countless ways and has already spilled over into sectarian street clashes, kidnappings and general government paralysis.(AP Photo/Hussein Malla)


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Activists say that Syrian security forces swept through two districts in Damascus on Wednesday, killing at least 31 suspected opposition fighters. The Associated Press reports that the army may have been targeting rebel teams that had been using the Nahr Eishah and Kfar Soussa neighborhoods to shell a nearby military airport.

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@ AP : Russia says Western powers are "openly instigating" opposition groups in Syria: http://t.co/Il6rHsxr -SC

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