Ministers have been accused of misleading the public over the controversial High Speed 2 rail development, as increasing numbers of MPs and senior business figures call for the multibillion-pound scheme to be scrapped.

Patrick McLoughlin, the transport secretary, claimed last month that a highly critical National Audit Office (NAO) inquiry, which calculated that the ambitious north-south rail link faced a £3.3bn funding gap, had used an "out-of-date analysis". In a television interview, the transport minister, Simon Burns, said he did not recognise some of the figures used in the report.

The Observer has established, however, that the data was approved by the Department for Transport's most senior civil servant before being published, and the figures were supplied by the transport ministry itself.

Ministers' decision to launch a rare attack upon an NAO report has angered members of the public accounts committee. They plan to raise the issue with Philip Rutnam, the transport department's permanent secretary, who approved the figures and who appears before the committee tomorrow.

Margaret Hodge, chair of the committee, which scrutinises public expenditure, said McLoughlin and Burns were joining a growing number of coalition ministers who were happy to rubbish official and factually accurate analysis. "I am fed up that ministers run away from the argument by denying the facts. There may be a good reason for going ahead with HS2, but justify it on the basis of facts, not by negative briefings against the truth," she said.

Hodge said the department's criticisms would be raised with Rutnam tomorrow. "We will expect the permanent secretary to fulfil his proper role as an accounting officer, which means he won't be motivated by political bias and will acknowledge the facts as set out in the NAO's report, which is based on departmental data."

The development comes after McLoughlin prompted further anger among Tory backbenchers when he admitted that HS2's budget had increased from £34.2bn to £42.6bn. Meanwhile, in last week's spending review, chancellor George Osborne announced £11.5bn of cuts to public expenditure.

McLoughlin's admission prompted John Cridland, head of the employers' group the Confederation of British Industry, to warn: "The case for judging this absolutely has to be value for money. At what point does it cease to be value for money?"

Rutnam wrote to the NAO at the beginning of May in accordance with usual protocol, expressing approval of the report's facts and methodology. "I am content that the detailed findings set out in the body of the report are fair and accurate and that the recommendations for future work are practical and appropriate," he wrote. Two weeks later, Rutnam sent another letter, which challenged the report's conclusions but not the figures within it.

Cheryl Gillan, the former Tory cabinet minister who has led a growing party rebellion against HS2, said the departmental response was typical of a government trying to rubbish serious questions raised by auditors. "[The government] has already made basic errors in accounting and engineering calculations and now has to completely rerun a flawed consultation on compensation. It is hardly surprising its competence to deliver a multibillion-pound project is seriously in doubt," she said.

The NAO report was highly critical of the government's plans, saying there was a lack of clarity about the department's objectives and that the need for the line had yet to be demonstrated. It also examined the transport department's estimated cost figures over four years to 2021, and found that the government had not yet decided how to pay for £3.3bn of them.

Work on the first phase of HS2, between Birmingham and London, is due to begin in 2017. The NAO report said the timetable was "challenging".

The report added that the economic benefits from HS2 had fallen radically during the planning process. In 2010, every £1 spent on the first stage of the line would have yielded £2.60 of benefits. Since then the figure had fallen to £1.40.

Ministers forced through a paving bill, granting funds for continuing work, last week despite facing increasing opposition, with 37 MPs, mostly Tories, signing a motion which aims to derail the plans.

A transport department spokesman said Rutnam's first letter sent in May was in reference to technical details within the report and that he had consistently disagreed with a conclusion drawn from old data that dates back to 2011.

"We have never accepted the conclusion of the National Audit Office report and have consistently said this. The report depends too much on out-of-date analysis and does not give due credit for all the good progress that has been made in the 18 months since the business case they examined was produced. Ministers are entirely in agreement with this position and we will continue to contest the NAO's conclusion," he said.

The spokesman added that Burns did not recognise the NAO's £3.3bn "funding gap" calculation.

"The case for HS2 is clear. Without it the key rail routes connecting London, the Midlands and the north will be overwhelmed. HS2 will provide the capacity needed in a way that will generate hundreds of thousands of jobs and billions of pounds of economic benefits," he said.