Harper did not spell out what Ottawa might do to prevent future ships full of migrants from arriving in Canadian waters similar to the way 492 Tamils arrived last week.
Public Safety Minister Vic Toews has been saying since last week that Canada will do whatever it has to do to beef up its laws and prevent human smugglers and terrorists from taking advantage of Canada's refugee system.
"Ultimately as a government we're responsible," Harper said following a local announcement in Mississauga, Ont.
"It's a fundamental exercise of sovereignty. We are responsible for the security of our borders and the ability to welcome people or not welcome people when they come."
Harper noted Canada is a land of refuge, but when hundreds of people come to the country outside the proper channels, it leads to "significant security concerns."
"I think Canadians are pretty concerned when a whole boat of people comes, not through any normal application process, not through any normal arrival channel, and just simply lands and obviously this leads to significant security concerns."
Toews has suggested Canada will work closer with its allies to prevent future ships from even setting sail. Australia has also grappled with migrants arriving on its shores by ship.
Having the Canadian navy turn the ships around and send them home is not an option, despite the demands of many readers commenting on news websites and in letters to the editor.
Canada is a signatory to a UN declaration requiring countries to process refugee claimants at home.
Liberal MP Marc Garneau called on the Harper government Tuesday to show more compassion for the migrants, urging Toews to "lower the tone" of the government's rhetoric.
Garneau said since the MV Sun Sea arrived last Friday, the government has been fixated on suspicions that the ship is part of an organized human smuggling ring and that some of its passengers may be terrorists.
The migrants include 63 women and 49 minors — some of them very young children — and Garneau said Toews needs to remember that many may be genuine refugees.
The migrants say they've faced persecution in Sri Lanka since last year, when a decades-long conflict between the Sinhalese government and separatist Tamil Tigers came to a bloody end.
The migrants claim to have escaped mass murders, disappearances and extortion.
But Toews has said among the migrants on the MV Sun Sea are believed to be terrorists and criminals. The Tamil Tigers are considered a terrorist organization in Canada.
"If you look at (the reaction of) Mr. Toews, there's a little bit too much on terrorism and human trafficking and not enough perhaps to indicate, I would say, a little bit of a level of compassion," Garneau told a news conference.
"So just a sense of proportion on this whole thing would be nice."
Garneau added that the Liberals agree the government should prevent terrorists and human smugglers from abusing Canada's generous refugee system.
He said the government shouldn't over-react, noting that the latest ship-borne arrivals represent only about two per cent of the refugee claimants who arrive in Canada each year, most of them at airports.
NDP immigration critic Olivia Chow said the best way for Canada to ensure no more migrant ships are on the way from Sri Lanka is to work on ending suffering in that country.
The NDP accused Ottawa of simply moving on from the Sri Lanka file after the bloody civil war ended there last year.
“What motivated these people to take such a dangerous journey is the violence, insecurity, mass detention and human rights violations that have been widely reported by independent observers,” said Chow.
In Vancouver, mandatory detention hearings for the migrants were under way.
One claimant, a young woman who came here with her mother, father and brother, was ordered detained after a lawyer for the Canada Border Service Agency said authorities had not confirmed her identity.
The woman, who has family in Toronto, had what she said was an original national identification card and a birth certificate. Agency lawyer Ron Yamauchi said the documents are still being inspected and the woman's interviews have not been completed.
Since undergoing medical checks in Victoria over the weekend, the migrants have been transferred to jails in the Vancouver area.
Detention hearings are usually held in private, but members of the media argued the hearings are in the public interest and should be open in this case.
Leanne King, a member of the Immigration and Refugee Board, agreed Tuesday, but with conditions. The migrants' names, ages, places of birth and other identifying details can not be reported.
King also denied a request from members of the Canadian Tamil Congress to also be allowed, saying they can get their news from reporters.
The hearings could give the public a better understanding of who the migrants are and how they chose to undertake a difficult, illicit and expensive journey across the Pacific.