The communities secretary, Eric Pickles, has said the Environment Agency made a mistake in not dredging the rivers in the Somerset Levels, and warned that flooding is likely to extend to the Thames valley by the middle of next week.

Speaking on the BBC's Andrew Marr programme, Pickles apologised on behalf of the government while continuing to pin blame on the EA. He said: "We made a mistake, there's no doubt about that and we perhaps relied too much on the Environment Agency's advice."

Asked if the prime minister should also apologise, Pickles said: "I'll apologise. I'll apologise unreservedly.

"I am really sorry that we took the advice … we thought we were dealing with experts."

David Cameron will be chairing another emergency meeting of Cobra on Sunday afternoon likely to be focused on the new threat to the Thames valley, protecting energy infrastructure, and ensuring improved bus and plane services are brought forward to replace the collapsed rail line to Cornwall.

Pickles said: "I don't think it was a question of money in the Somerset Levels. It was policy and it was a policy not to dredge and the more we know about it the more we know it was a wrong-headed decision. It's now accepted even by the Environment Agency that was a mistake and we made a grave error."

Pickles also rejected calls by the Ukip leader, Nigel Farage, for some of the overseas aid budget to be transferred to pay for flood prevention and to help those whose homes and farms have been damaged. Pickles said Farage was having "a cheap populist hit".

Farage, who is visiting Somerset, said "charity should begin at home". "Would it not be a good gesture if we had a British government that put its own people first? We have got sea walls that need maintaining. It is going to need more than the paltry money has been offered so far." He said the government had offered less than 1% of the overseas aid budget, adding that of the £11bn spent overseas only £2bn was spent on humanitarian projects.

He said he wanted a public inquiry into the flooding, which he said should examine the extent to which the EA was being directed by European Union directives.

Pickles chastised the chairman of the EA, Lord Smith, saying he would not be wearing a "save Chris Smith" T-shirt if the peer decided to quit.

Asked if Smith should quit, Pickles said: "Its a matter for him. It has been an unhappy time for Lord Smith and no doubt his lordship is reflecting on the feedback he has got from the people of Somerset. At least the Environment Agency will not need to organise a focus group to understand what people think."

Pickles and the rest of the government are furious with the EA for not dredging the rivers on the Somerset Levels, insisting the agency cut back on dredging as a matter of policy rather than because of a lack of funding, making it more difficult for the flooded water to flow out.

Smith's tenure as chairman of the EA ends in the summer.

Speaking on the Sky News Murnaghan programme, Pickles also accused David Jordan, the director of operations of the EA, of "having a tin ear" when he suggested the agency had been successful in fighting the floods. "If you are stuck on the Levels, that kind of remark is going to grate," Pickles said.

Pickles has taken over the government effort to combat the flooding after the environment secretary, Owen Paterson, stepped back from the frontline to have an eye operation.

The communities secretary said he would be visiting the Levels in the middle of the week, but his attention seemed focused on the Thames valley, where he said flooding was now inevitable because rivers were full.

Gatwick airport in West Sussex has doubled the number and increased the size of planes from the south-west, but there are also calls for an urgent diversion of the main rail line, with some of the money coming from the cash earmarked for HS2.

Pickles showed little interest in whether the flooding had been caused by climate change, as suggested by the Met Office at the weekend. Pickles said the Met was merely suggesting that climate change might be responsible. Pickles said: "It does not matter if it is climate change or a fluctuation in weather patterns," adding that he was not qualified to comment on the ultimate cause.