John Greyson, a Toronto-based filmmaker and York University professor, and Tarek Loubani, a doctor in London, Ont., were in Cairo and on their way to Gaza on Friday when they were arrested by Egyptian police.
The federal government has yet to be told on what basis Egyptian authorities detained the pair, Harper said Monday during a news conference in Whitehorse.
"We are obviously extremely concerned about the arrest and treatment of the two Canadian citizens who have been detained in Egypt," Harper said.
"We don't frankly know what evidence supports any such arrest, and we have expressed our concerns directly to the Egyptian government."
But it appeared to be a case of "two people being in the wrong place at the wrong time," junior foreign affairs minister Lynne Yelich said in an emailed statement.
Yelich also posted on Twitter that the Canadian ambassador in Cairo paid a visit Monday to the Egyptian Foreign Ministry, demanding that Egyptian authorities explain the detentions.
A number of other diplomatic levers were being pulled by the government to seek their release and to obtain more information.
A source at the Department of Foreign Affairs said Egypt's ambassador was summoned to meet Monday with senior Canadian officials in Ottawa to discuss the detentions.
The Canadian ambassador in Egypt met with the pair Sunday in the Cairo prison where they are being held and consular officials were expected to meet with them again Monday.
Although Canadian consular staff have been in contact with the pair, Egyptian authorities have yet to justify their detention, said Justin Podur, a friend of both men.
Greyson's family says in a statement that they're confident the Canadian embassy in Cairo is doing "everything they can" to free the pair.
In the same statement, Loubani's brother said that while he recognizes Egypt is going through a painful transition, detaining a doctor and filmmaker without due process is "clearly a step in the wrong direction."
"The Egyptian transitional government has frequently repeated its commitment to democratic values and the rule of law," said Mohammed Loubani.
"The continued detention of John and Tarek clearly falls short of that commitment."
Two medical groups, a film festival organization and York University are calling for the release of the two Canadians. Thousands of people have also signed an online petition demanding that the pair be set free.
The Medical Reform Group said it's astounded that Loubani and Greyson are being detained, and is urging the Conservative government to take all actions necessary to ensure their release.
"It is completely unacceptable that Dr. Loubani and Mr. Greyson should continue to be detained," the Toronto-based group said in a statement.
"The Canadian government must do everything in its power to get them free."
The sentiment was echoed by Calgary-based Canadian Doctors for Medicare.
York University said that Greyson is a valued member of the York community, where he has taught film and video theory, film production and editing in the university's film department since 2005.
A petition launched on the website Change.org had more than 4,700 signatures by late morning Monday.
Others have taken to Twitter and other social media sites to demand action from Foreign Affairs Minister John Baird.
Tensions in Egypt continue to escalate following the ouster of Islamist President Mohammed Morsi in early July.
In all, nearly 1,000 people have been killed in violence between security forces and supporters of Morsi since last Wednesday.
No reasons have been given for the detention of the two men, although Loubani and Greyson are no strangers to activism.
In July 2003, Loubani was arrested by the Israeli police while working as an observer on human rights abuses in the Palestinian territory with the group International Solidarity Movement.
Loubani alleged at the time that he and other observers were beaten and tortured while behind bars.
A little over a year ago, the emergency room doctor interrupted then-Human Resources Minister Diane Finley during a speech to protest government cuts to health care for refugees.
Greyson joined protesters aboard the "Tahrir" in 2011 as a Canadian member of the so-called Freedom Flotilla II, which had planned to break a maritime blockade of the Gaza Strip by Israel.
Greyson's film works, which often feature anti-homophobia themes, have also often been controversial.
His work includes "The Perils of Pedagogy," "Kipling Meets the Cowboy" and "Moscow Does Not Believe in Queers." In 1988, he released his first feature film, "Pissoir," in response to police raids on men in public washrooms, parks and gay bathhouses.
The Toronto Palestine Film Festival said in a statement Monday that Greyson and Loubani are known internationally for humanitarian work in their respective fields.