The move follows two weeks of negotiations between the Department of Family Services and the board at Osborne House to resolve health and safety issues at the shelter.
The provincial government had ordered the shelter to come up with a plan to resolve the issues, but says independent consultants deemed the board was unprepared to do so.
Marlene Bertrand, a family violence prevention expert, has been appointed provisional administrator of the facility.
Staff is not affected as the executive director is already on medical leave, but the remaining board members have effectively been fired.
Osborne House is the largest of 10 domestic violence shelters in Manitoba with just over $1.6 million tax dollars funding its operations.
The Manitoba government says there are problems with the level of counselling at the shelter and the front-door security is lacking. It also says a possible case of child abuse was not reported to authorities.
The NDP government has been embroiled in a nasty spat with the shelter that has involved accusations of racism, political favouritism and a toxic work environment.
Osborne House C-E-O Barbara Judt has insisted the NDP is targeting the shelter partly because she attended a news conference with the opposition Progressive Conservatives in the 2011 election campaign when the Tories promised $5 million to upgrade the shelter.
And in an email last year, Aboriginal Affairs Minister Eric Robinson denounced a burlesque show that raised money for the shelter.
Robinson wrote to a government employee that the theme was inappropriate and demonstrated "the ignorance of do-good white people.''
The comments only came to light this summer, after Judt obtained them under a freedom-of-information application for government documents related to the shelter.
The comments might never have come to light, because the government blacked them out with a marker. But the marker didn't fully cover Robinson's words. They were visible when the documents were held up to a light.
Robinson initially said he would not apologize for the remarks, then issued a written apology for his choice of words. The Opposition Progressive Conservatives have called on Premier Greg Selinger to reprimand Robinson, but Selinger has stood by his minister, saying he has done a good job in cabinet.
(CJOB, The Canadian Press)