Stephen McNeil said his Liberal government submitted a letter Thursday asking for an audit to be completed some time during the 2014-15 fiscal year.
"We know this has been a boondoggle," he said after a cabinet meeting. "From the day we came into power, we've dealt with this. Our number 1 focus is to get that boat in the water (this spring). This is a Nova Scotia icon. It's a Canadian icon."
The high-profile project has been bogged down by lawsuits, management infighting and political theatre, which the premier blamed on the previous NDP government.
He said his government is also poised to unveil a new website intended to answer frequently asked questions about the troubled project.
As well, he said a mediator has been called in to settle disputes between the project manager and the shipbuilding consortium hired to do the work.
"There's been a mentality in the last few years of, 'Let's sue everybody and fight with everybody,'" McNeil said.
McNeil's government has had to deal with a series of tough questions about the Bluenose II project since the Liberals were elected to govern in October.
In December, questions were raised about rising project management costs, prompting the heritage minister to call for some kind of review.
Earlier this week, the Canadian Taxpayers Federation released documents showing the Lunenburg-based consortium rebuilding the vessel has routinely added hefty markups on the bills it submits to the provincial government.
Progressive Conservative Leader Jamie Baillie has been pressing the Liberal government to explain and clean up the political mess left by the previous government.
On Wednesday, Baillie submitted to McNeil a list of 55 questions about the Bluenose II after the Liberal majority on an all-party legislative committee voted down an opposition bid to have the cost overruns examined.
Baillie said he's glad the auditor general will be stepping in.
"I'm glad ... because we've been asking these questions all week," he said. "But I want to make sure that this is done in a timely way and that the results are there for all Nova Scotians to see."
The original budget for the project was $12.5 million. The latest estimate stands at $16.7 million, but the government has admitted labour costs will push that amount higher.
The Bluenose II, launched in 1963, is a replica of the original Bluenose, the 1921 Grand Banks fishing schooner that won worldwide acclaim for its graceful lines and speed.
Nova Scotia's 43-metre sailing ambassador was supposed to return to regular sailing in the summer of 2012 after an extensive two-year rebuild.