Wes Sheridan said he is concerned about the direction Ottawa is going in areas that affect provincial jurisdiction, including the Canada Job Grant, cuts to the Immigrant Investors Program and a promise to allow income splitting in the future.
Extra money to allow the Atlantic Canada Opportunities Agency to spend on commercial projects pleased Sheridan.
He said the province has been spending money on innovation since 2007.
And while he applauded the federal government for its decision to provide two additional years of funding for the Wood Islands ferry between P.E.I. and Nova Scotia, Sheridan said a long-term funding plan is needed for the service.
But he accused Ottawa of balancing its books by leaning on the provinces.
"While it is positive to see that the federal government has balanced its budget, our concern is that in their attempt to find positive measures, they are finding the initiatives and the funding within provincial jurisdiction," he said in a statement.
The federal government's decision to push ahead with the Canada Job Grant in April was also a concern to Sheridan, who said more negotiations are needed to come to a solution on the program that satisfies all levels of government.
"We were alarmed to learn the Immigrant Investor Program would be ended without warning, and we were offered a take it or leave it Canada Jobs Grant program," he added.
"Provinces and territories have provided a reasonable, unanimous counter-proposal for the Canada Jobs Grant that invests in training, while protecting the most vulnerable. It is our hope that the federal government accept it rather than create a new bureaucracy to deliver this program."