Harper is travelling to the large General Assembly gathering ostensibly for meetings on Libya and child and maternal health.
On Friday, the prime minister was drawn into the brewing showdown over the Palestinian bid for statehood recognition at the UN.
"We view this unilateral action on behalf of the Palestinian Authority to be not helpful," Harper said during a stop in Saskatoon.
"No unilateral actions like this are helpful in terms of establishing a long-run peace in the Middle East. Canada views the action as very regrettable and we will be opposing it at the United Nations."
Foreign Affairs Minister John Baird, who will be accompanying Harper to New York, has already expressed Canada's opposition to the Palestinian plan. Canada supports a two-state solution to the conflict but only after a negotiated settlement between the Palestinians and the Israelis.
The prime minister is not expected to address the General Assembly, and will leave that duty to Baird the following week.
Palestinian president Mahmoud Abbas said Friday he will ask the UN Security Council to endorse his people's statehood bid next week.
Abbas emphasized that he did not intend to isolate Israel. But the plan sets the UN stage for a diplomatic showdown. The United States has indicated it would veto the measure in the Security Council.
The Palestinians say they are turning to the UN after years of frustration with Israel. Any recognition would be symbolic, but the Palestinians hope the elevated stature would give them more clout in future negotiations with Israel.
"We don't want to raise expectations by saying we are going to come back with full independence," Abbas told Palestinian leaders. He said he was going to the United Nations to "ask the world to shoulder its responsibilities" by backing the establishment of a Palestinian state in the West Bank, Gaza Strip and east Jerusalem.
Abbas urged the Palestinian people to refrain from violence, saying "anything other than peaceful moves will harm us and sabotage our endeavours."
Israel has mounted a full diplomatic counteroffensive to the Palestinian statehood bid, and will be looking to the Harper government — one of its most steadfast international allies — among others to thwart the Palestinian aspirations.
"The Palestinians seek to isolate Israel diplomatically at a time when its peace agreement with Egypt is being threatened by extremists and relations with Turkey are also in crisis," said a widely-distributed email by the Washington-based Israel Project lobby group.
"This resolution may well create instability and violence on the ground by creating exaggerated expectations among the Palestinians that cannot be fulfilled. The storming of the Israeli embassy in Cairo last weekend illustrated how easily events can spiral out of control."
The diplomatic battle threatens to cloud more positive international developments, which Harper hopes to highlight.
The General Assembly voted Friday to formally gave Libya's National Transitional Council the country's seat on the world body. The council led that rebellion that toppled dictator Moammar Gadhafi.
A senior council official will now be able to speak for Libya at next week's ministerial session of the General Assembly, and also participate in meetings.
The resolution was approved by a vote of 114-17 with 15 abstentions.
Harper will meet with fellow world leaders for a so-called "friends of Libya" meeting.
That will allow Harper to get an update from British Prime Minister David Cameron and French President Nicolas Sarkozy, who both travelled to Libya this week.
Harper will also co-chair a session of the Accountability Commission on Women's and Children’s Health.
The initiative to help poor mothers and children in the Third World was the prime minister's signature pledge of the Muskoka G8 summit he hosted last year.
"Canada continues to play a leading role on the world stage — from improving the health of women and children in developing countries, to assisting the Libyan people in their transition to democracy, to demonstrating fiscal leadership and strong fundamentals in tough economic times," Harper said in a statement Friday.
"I look forward to working with our international partners in New York so we can continue to generate concrete results on these important issues."
—With files from The Associated Press