Prime Minister Stephen Harper has dismissed a number of key recommendations made by the head of the federal sponsorship inquiry that would have reduced some of the power of the Prime Minister's Office and protected civil servants from political interference.

When Justice John Gomery's report was released 10 months ago, Harper only said he thought the proposals had merit.

But in a public letter released Wednesday to 65 senior officials who had opposed Gomery's call for better insulation of civil servants from politicians, Harper expressed for the first time his reservations about several proposals made in Gomery's scathing report.

"Our approach has been to assess the merits of Mr. Justice Gomery's recommendations on a case-by-case basis and there are a number of areas where my government finds itself unable to agree with Mr. Justice Gomery," Harper wrote in his seven-page letter.

Harper targeted Gomery's recommendation of changes to the role of the Clerk of the Privy Council, which would see the position's duties split to prevent the bureaucrat responsible for the prime minister's department from also being in charge of rating the performance of other senior civil servants.

'There are a number of areas where my government finds itself unable to agree with Mr. Justice Gomery'-Prime Minister Stephen Harper

"[T]he Clerk's role as Deputy Minister to the Prime Minister and Head of the Public Service are also vital to the sound functioning of our system of government," he wrote.

Harper said a modern prime minister "faced with a sweeping range of complex demands" needs the clerk to offer "co-ordinated, professional" public service advice on policy and operations.

Harper also said it would not be "an appropriate role" for deputy ministers — the senior bureaucrats in government departments — to be insulated from political control by making them answerable to Parliament if laws or government rules are broken.

"I also share your view that the public service, a recognized and essential institution of government, exists to provide professional advice and operational support for the government of the day and does not exercise authority independent of government," he wrote.

"Ministers alone are accountable to Parliament, which is a central tenet of our system of responsible government."