The Mounties have been going in and out of Caspian Construction on McGillivray Boulevard since about noon Wednesday.
Caspian is the main contractor involved in the conversion of the former Canada Post building on Graham Avenue into the Winnipeg Police Service's new HQ, which has gone $75 million over budget.
At one point, plainclothes officers emerged from the company's office with at least two computers.
According to RCMP, the police headquarters investigation began after the Manitoba government referred three audits to police in August for review.
Investigators from the RCMP's federal, serious and organized crime units have been working on two separate reviews: one involving the WPS headquarters and another involving Winnipeg Fire Paramedic stations.
"The RCMP have completed a review of the forensic audit regarding the construction of the Winnipeg Police Service Headquarters and this is now considered a full investigation. The Winnipeg Fire Paramedic stations file is still under review," according to a news release.
RCMP say their execution of the search warrant "at a local business" on Wednesday is related to the investigation, but they would not release further details.
'We've inherited this nonsense,' says mayor
Bowman told reporters on Wednesday afternoon that he welcomes the RCMP investigation, as Winnipeggers want answers about what happened.
He said the Mounties must be allowed to carry out their investigation, and the city promises full co-operation.
Legal counsel will help the city in looking at Caspian Construction's status with regards to the police headquarters project, he said.
The mayor added that when the RCMP investigation is finished, his office will move to fire anyone from city staff who was involved in any wrongdoing.
"We've inherited this nonsense," said Bowman, who succeeded Sam Katz as mayor this past fall.
River Heights-Fort Garry Coun. John Orlikow said he doesn't know any details about the police raid at Caspian, but he welcomes the investigation and echoed Bowman's commitment to get answers.
"We're going to continue the work we have to do here internally at city hall to make sure that we restore the public's trust," he said.
Former St. Boniface councillor Dan Vandal, who is now a federal Liberal candidate, said on Twitter that he is "sad it has come to this" but he's glad that council sent the matter to Manitoba Justice.
Follow live updates on the police headquarters probe from CBC reporter Sean Kavanagh: