The transport secretary Patrick McCloughlin could be hauled before MPs to explain why he commissioned a £70,000 report into a possible buyout of Manston Airport by Thanet council.

The threat comes after letters reveal that the Department for Transport's most senior civil servant questioned him formally about why it was necessary.

It is an embarrassing development for the government in the Manston saga, which may see the minister summoned to appear before the Public Accounts committee.

In a highly unusual move, the Permanent Secretary wrote to the minister to outline concerns about the costs and probity of the decision to appoint consultants to examine Thanet council's decision not to pursue a CPO.

In the letter, Philip Rutman told the secretary of state he was writing in his capacity as the accounting officer: "For an action to be judged good value for money, one must expect the benefits to exceed the costs, and take careful account of the risks.

"Having considered the matter carefully, I think it is unlikely that the appointment of consultants as proposed will provide good value for money. The government has no defined role at this stage of the CPO process. Nor is there a clear and obvious gap in the process which would typically fall on a Department to fill."

The letter goes on to say he is unclear what the rationale for the report is and questions the costs.

"The cost of this review is not large by the standards of DfT's budget but it is still a material sum. In light of my reservations I am therefore seeking a written direction from you to proceed with the award of the contract to consultants to undertake the review of papers as described."

Effectively, the permanent secretary was forcing the minister to order him to carry out the study and commission consultants despite his qualms.

In a reply, the secretary of state writes that he believes there are grounds for an analysis of the papers.

"I have noted your concerns about the value for money of undertaking such a review. However, I believe there are wider issues to consider which I accept fall outside the remit of the accounting officer but that I consider are relevant.

"Our own Aviation Policy Framework highlights the importance of airports in encouraging investment, exports and in creating local jobs. Smaller airports in particular can often be key to providing regions with convenient access to other national and international markets."

He says that given the 150 jobs at the airport that were lost, there were "strong local concerns" and that the government should be willing to use its resources to help Thanet council.

As it happens, the long-awaited report concluded that the council could have done more to assess the proposal by the American consortium RiverOak to act as Thanet council's indemnity partner but was neutral on the the issue of whether a CPO should have been pursued.