Iain Duncan Smith has blamed civil servants for IT failings in the introduction of the £2.4bn universal credit system, which is designed to consolidate six welfare payments into one.

The work and pensions secretary took the rare step for a cabinet minister of publicly blaming civil servants after the release of a scathing report by the National Audit Office (NAO) on the introduction of universal credit. The report said the welfare changes had been poorly managed and were riddled with major IT problems, threatening to increase costs by hundreds of millions of pounds.

Duncan Smith told BBC Breakfast he had "lost faith in the ability of the civil servants to be able to manage this programme" and the vast IT development involved.

He told the Today programme on BBC Radio 4: "I fully accept, because I could have written this report myself, that the problem was that those charged with putting together the detail of the IT – we rely on people telling us that is correct – did not make the correct decisions. But we intervened to change that and all the programme directors from outside have said we did the right thing. Even the report says this is the right process."

Duncan Smith blamed the initial IT team for failing to raise concerns. "What went wrong with the universal credit team – and they [the NAO] are right about this – there was a sense that somehow they just wanted to be able to say it was all going well. And that was the key problem.

"I agree with that, which is why in 2011, with my concerns, I changed the programme to introduce a pathfinder and why in 2012, after my own independent review told me that my concerns were justified, we made changes to personnel and brought in outside people."

Duncan Smith said Howard Shiplee, the construction director for the London 2012 Olympics who was brought in earlier this year to lead the delivery of universal credit, had said the project would be delivered on budget and on time. "The overall timetable of 2017 – we will deliver this in that timescale. It is a very important reform and it is a reform that will both save the government and taxpayers money and improve the lot of those most needing it."

The NAO said the universal credit project had been beset by "weak management, ineffective control and poor governance".

Ministers have already written off £34m wasted on failed IT programmes for the project run by the Department for Work and Pensions and may be forced to delay its national launch beyond 2017, the NAO said.

Universal credit merges six different benefits, with the claimant receiving a single monthly household payment. It requires different payments to landlords, more online claims, and merges in-work and out-of-work benefits, requiring new definitions of benefit conditions for those in work. It also requires close co-operation between the DWP systems and tax officials at HM Revenue & Customs.

It was initially planned that the project would be introduced nationally by October this year, but pilot projects were delayed and are now going ahead in four areas.

The report was seized upon by Labour as evidence that Duncan Smith has covered up significant problems that could put welfare claimants and their families at risk. Liam Byrne, the shadow work and pensions secretary, described universal credit as a "Titanic-sized IT disaster".

In urgent parliamentary questions on Thursday, Byrne told the House of Commons that the top civil servant at the DWP had confirmed to him that the timing of the entire programme may have to be put back.

"To hit his [Duncan Smith] deadline at the end of 2017 he must now move over 200,000 people a month on to the new system, that is a city the size of Derby," Byrne said. "He has lost control of the programme and he has lost control of the department … The quiet man must not become the cover-up man."

The work and pensions committee chair, Dame Anne Begg, accused Duncan Smith of bullish behaviour and said he should "stop over-promising what can't be delivered".

Duncan Smith told the house that he took "full responsibility for the delivery of this. I will not shirk that," and retorted that it took determination to complete a project of this size.

"I'm not being over-bullish about this. The reality is it takes determination to drive a reform through. I have that determination and the department is determined, with support and help, to make this happen."

He said he could not give figures for how many would be in receipt of the benefit by the election in 2015 but added that he was seeking to shut down other types of payments in the next two years.

"I am looking to close down jobseeker's allowance and tax credits well in advance of the election," he said.

In March 2013 Duncan Smith told parliament universal credit was "proceeding exactly in accordance with plans". However, the report outlined how the project was "reset" a month earlier following the involvement of the Major Projects Authority, which has the power to intervene on behalf of taxpayers.

The auditors' report also found the government had not achieved value for money on its spending up to the end of April, most of which was spent on building IT programmes which could handle data for 184,000 claimants. Of the £303m spent on IT, £34m had been written off and the systems still had limited functionality.

Margaret Hodge, the chair of the public accounts committee, said: "The DWP seems to have embarked on this crucial project, expected to cost the taxpayer some £2.4bn, with little idea as to how it was actually going to work."

The NAO found the IT system could not identify potentially fraudulent claims, meaning manual checks were needed. "Such checks will not be feasible or adequate once the system is running nationally. Delays to the introduction will reduce the expected benefits and – if the department maintains a 2017 completion date – increase risks by requiring the rapid migration of a large volume of claimants."

Civil servants were also accused by the watchdog of having weak control of the programme and were unable to assess the value of the systems on which more than £300m had been spent.

"These problems represent a significant setback to universal credit and raise wider concerns about the department's ability to deal with weak programme management, over-optimistic timescales, and a lack of openness about progress," it said.