MPs have criticised the government’s response to a report that investigated the problems with the Rural Payments Agency (RPA) IT system.

A Commons committee report earlier this year criticised the way the agency was pressured into proceeding with the computerisation of its system for paying farm subsidies resulting in huge delays paying farmers and a looming EU penalty, despite receiving ‘red lights’ on Gateway progress reviews.

The committee said it was unfair to make a scapegoat of RPA chief executive Johnston McNeil because he was not solely responsible. The committee members were ‘astonished’ that the then-Department of Environment, Food and Rural Affairs (Defra) permanent secretary Sir Brian Bender retained his rank, and challenged the way Defra Secretary of State Margaret Beckett was ‘rewarded’ with promotion to Foreign Secretary - she eventually left office in the reshuffle when Gordon Brown became prime minister.

The government response said Commons committees had no business acting as disciplinary tribunals and regretted it had criticised named civil servants – a statement the committee has denounced as ‘shoddy.’

The department is alleged to have cut its flood defence budget to make up some of the costs.