It comes decades after women — many of them drug addicted sex-trade workers — began disappearing from the impoverished neighbourhood.
Assistant Commissioner Craig Callens told a news conference Friday he wanted to tell victims' families "how very sorry we are for their loss."
"I apologize the RCMP did not do more," said Callens, who became the top RCMP officer in charge of B.C. last month.
"I would like to be very clear this morning. As the commanding officer of the RCMP in British Columbia, I believe that, in part, with the benefit of hindsight, and when measured against today's current investigative standards and practices, the RCMP could have done more."
The frank admission is appreciated by Ernie Crey, the brother of Dawn Crey, one of the women on the missing and murdered list.
"I'm glad they manned up to it. They've owned up to it."
But it's the statement that Mounties regret not being able to lay charges sooner against Pickton that resonated with Crey.
"If they had done more, my sister — in spite of her mental illness and her addiction to street drugs and living a life on the fringe— she may have been alive today and that would go for some of the other women as well."
Dawn Crey's DNA was found on the Pickton pig farm, but he was never charged with her death. He was accused of 26 murders and was finally convicted of killing six women.
The apology comes just over two weeks after the first RCMP witness testified at the public inquiry into how the RCMP and the Vancouver Police Department handled the missing women investigation.
During the hearings, Cameron Ward, a lawyer for several family members, asked RCMP Supt. Bob Williams if Mounties were prepared to apologize for the way they handled the case.
He replied that it would be up to the deputy commissioner in B.C. to make such a statement.
Williams was asked to write an internal review of the investigation in 2002 in advance of a civil lawsuit and concluded no major mistakes were made.
Callens said it was that testimony that brought the issue to his attention.
"It became obvious that it was something that needed to be addressed now, as opposed to at the conclusion of the inquiry."
British Columbia has legislation called the Apology Act, which allows a person to make a full apology without the statement being used as an admission in a civil lawsuit.
Inquiry commission counsel Art Vertlieb said the apology may change the tenor towards the RCMP at the inquiry, because it's clear that the failure of RCMP to respond was of great aggravation to the families.
"Where it's important is not to be critical that it's belated, but to accept it and say this may help commissioner (Wally) Oppal have an attitude shift that will allow the RCMP to participate in, frankly and openly, discussing mistakes that were made."
Callens said his department will apply the recommendations from the Oppal commission to improve policing services in B.C.
The inquiry has heard Pickton could have been caught sooner if both the Vancouver Police and the RCMP had taken the disappearances more seriously.
Vancouver police apologized in 2010, but the RCMP had not. Instead, Callens' predecessor, then-deputy commissioner Gary Bass, issued a statement of regret.
Callens said the RCMP's investigation practices have improved since 1998.
"As the inquiry progresses, I expect there will be a good deal of information shared that identifies what is different today in 2012 in the way in which the RCMP specifically, and police generally, conduct these types of investigations."
While Callens hadn't contacted each individual family, he said he soon would.
Crey said the apology may mean a new start between police, family members and the residents of the Downtown Eastside.
"I don't want to go on into the future nursing these feelings of anger and suspicion about these police agencies."
It may even bring some peace, Crey suggested.
"We'll always live with it, right. The feelings won't be expunged, but it needs to be done. The policing agencies need a new relationship with the families of the murdered and missing women."