The trade union representing government scientists has demanded an apology from communities secretary Eric Pickles, after the stand-in floods minister blamed the Environment Agency's advice for the floods crisis.

Mr Pickles assumed the role of floods minister last week when environment secretary Owen Paterson was rushed to hospital for emergency treatment on a damaged retina.

But speaking yesterday, Mr Pickles sad the government's mistake had been to rely on expert advice from the Environment Agency.

In response, Leslie Manasseh, deputy general secretary of the Prospect trade union said: ‘In a single comment, he [Mr Pickles] wrote off a whole swathe of specialists, whose expertise has served government and the UK well.'

‘Staff are astonished to be scapegoated like this when any failings should be laid fairly and squarely at the doors of the government,' Mr Manasseh added.

He said budget cuts had starved the Environment Agency of vital investment and led to a reduction in the number of experienced flood engineers.

Mr Manasseh added that there would be less cash available for flood defences this year than at the time the Coalition was formed in 2010 and that the programme of 1,500 job losses at the Agency was on course.

Prospect negotiator, Kevin Warden said: ‘The policy of not dredging rivers in the Somerset levels is a case in point. 

‘It was made and endorsed by the minister at the Department for Food and Rural Affairs,' he added.

‘Pickles should apologise for the government's failings and let our staff get on with using their specialist expertise to help the public at this time of crisis.'

Under fire Environment Agency chair, Lord  Smith, has also taken to the airwaves today to defend the organisation's record.  He has claimed only a maximum of £400,000 was available for dredging the Somerset Levels area under rules set by the Treasury.

Writing in The Guardian, Lord Smith, the former culture secretary, wrote: ‘In a lifetime in public life, I've never seen the same sort of storm of background briefing, personal sniping and media frenzy getting in the way of decent people doing a valiant job trying to cope with unprecedented natural forces.'

BBC reports have also intimated that environment secretary, Owen Paterson, has appealed to the prime minister in the strongest possible terms to complain at Mr Pickles' grandstanding over the floods crisis.

The next meeting of the COBRA committee, which co-ordinates national responses to disasters and emergencies, is scheduled to be held this afternoon at 4pm – again chaired by the communities secretary.