The deputy chief executive of the NHS has admitted the Department of Health should have acted sooner over failings at Mid Staffordshire Foundation Trust, but blamed the Healthcare Commission for not warning them of the seriousness.

The inquiry was shown one of a series of letters sent by the HCC to the trust and the DH, while the investigation was still ongoing during 2008, raising serious concerns about staffing levels.

David Flory, who at the time was director general of finance, performance and operations, told the inquiry if the letter had been about an NHS trust, rather than a foundation trust, the DH would have ensured “action was taken quickly”. He said with a foundation trust they were reliant on the HCC recommending Monitor put the trust into special measures.

“There was a whole stream of information [during 2008] during which the people responsible for the HCC, the chair and chief executive at the top of the organisation, were not flashing serious concerns or warning about what they were finding… we were guided by the HCC,” he said.

He accepted the attitude at the time was one of waiting for the HCC to formally report but said looking back the time between the launch of the investigation and the publication of the report had been too long and action should have been taken sooner

Asked why the DH had subsequently seen fit to intervene to appoint a new chief executive at Mid Staffs, after the publication of the HCC’s report in 2009, he said the size and significance of the failure meant it was impacting on the reputation of the rest of the NHS.

The inquiry was shown a note written by Mr Flory in February 2009 suggesting it would be “reasonable” for trust chief executive Martin Yeates to “move to another post in the system”.

At the time Mr Flory had read the HCC report, however he told the inquiry he had changed his mind about Mr Yeates continuing to work in the NHS soon after the note was written when he received an addendum to the report.

Asked about the broader phenomenon in the NHS where managers of failed organisations move into new jobs or leave with big pay offs, Mr Flory said he had received significantly fewer requests to sign off exit deals since the case of Maidstone and Tunbridge Wells Trust.

Health secretary Alan Johnson intervened to prevent MTWT chief executive Rose Gibb leaving with a financial settlement days before the publication of a report highlighting exceptionally high number of c-diff cases.

Ms Gibb  later won £190,000 on appeal, but Mr Flory told the inquiry the fact the DH was seen to be “trying to do the right thing and not just pay off people for an easy life” had acted as a deterrent.

Mr Flory also criticised NHS West Midlands in his evidence to the inquiry for being “too easily assured” by Mid Staffs’ explanations for its repeatedly high hospital; standardised mortality ratios.

Asked why the Department of Health did not have in house HSMR analysis but instead paid the private company Dr Foster to do it, Mr Flory admitted it was “a very uncomfortable position for the department and the department has sought to change that.”

In his closing comments, Mr Flory told his inquiry he approached his job differently following the “scandal” of Mid Staffs.

He said: “I think it’s an important responsibility for leaders in the system to learn and to improve and to reflect on what can be done.”