The shuttering of the Kitsilano base announced last year has prompted demands from Premier Christy Clark and Vancouver Mayor Gregor Robertson for the government to change its mind, saying the move puts lives at risk.
But Harper said Friday his government is allocating its resources in a way that is best for the public.
"The paramouncy of government resources in this area is on public safety and the government is allocating its resources in a way that we believe, based on the advice we have received from the coast guard, that is best in terms of public safety," the prime minister said.
"That is to put as many of the resources as we can into actually having rescue boats in the water. That's where we put our investments going forward."
The Kitsilano base is in the heart of Vancouver's waterfront and is considered the busiest base in Canada, responding to more than 350 calls per year.
Its closure was announced last spring along with the closure of three other B.C. coast guard communication centres as part of the government's deep budget cuts.
Critics have said the decision to replace the base with a three-person inshore rescue team in Stanley Park for the peak boating season still amounts to what Clark called "a dangerous drop in service."
"The federal decision to close the Kits Coast Guard base was disappointing to say the least,'' Clark said in a video posted on YouTube last month.
The base, which is slated for closure this spring, responded to 271 calls in 2011 — 36 of them marine distress calls and 40 humanitarian distress, according to the Coast Guard.
When it closes, calls will be handled primarily by the Coast Guard base at Sea Island, in Richmond. That station will be getting a new hovercraft to allow faster response to localized calls.
Critics have argued that it would take at least 30 minutes for rescuers from Sea Island to reach those in distress around the Vancouver harbour, while those at the Kitsilano coast guard station would take only five to 10 minutes.
Jody Thomson, Deputy Commissioner of Operations for the Coast Guard, has acknowledged the closure will have an effect, but she has said reaction times will remain within international standards.
Clark is among the critics who say closing the busiest Coast Guard base in Canada will cost lives.
"Our swimmers, boaters and our ports expect the federal government to keep B.C.'s harbours safe. That's why we are asking them to reconsider the decision to close the base.''
But Harper said his government has instead put its money toward services the enhance public safety.
"We've made investments here and in other parts of the country precisely in that way, to try and move things away from offices and back offices and to actually having resources on the ground and in the water. That's what we're doing and that's we think is best for public safety."
Clark said last month her government is working at balancing B.C.'s budget and she understands the challenges, "but not when lives are at risk.''
Just over a month ago, Vancouver's police and fire chiefs wrote to Prime Minister Stephen Harper to express their concerns.
Vancouver Mayor Gregor Robertson is also fighting to keep the base open
Robertson has said there's a good chance people will die if the facility is closed and relocated to Sea Island in Richmond, B.C.
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