Up to £125m could be available for the North of England after Northern Powerhouse minister James Wharton performed a U-turn on asking Europe for help.
With just three days to go until the deadline for applications to the EU Solidarity Fund the Government is now filling out the paper work.
However critics say months of Conservative party wrangling on the EU referendum has delayed applying for the money, and Mr Wharton himself is campaigning to leave the EU.
Responding to an urgent question in the House of Commons tabled by Labour MP for Stockton North Alex Cunningham, Mr Wharton said: "The UK Government will make an application to the European Union Solidarity Fund.
"The EUSF was set up to respond to major natural disaster, the fund was created as a reaction to the severe floods in Central Europe in 2002.
"The Government has been working on this application for some time."
He said it could be used for compensation to communities but warned money could take months for it to appear.
Explaining delays, he claimed Scotland had been slow in providing the necessary information and they had been weighing up whether the EUSF would lead to a net benefit for the tax-payer due to costs of administering and delivering the fund.
Labour MP Holly Lynch welcomed Mr Wharton's announcement and commented how 'awkward' it would have been for Mr Wharton, who wants to leave the EU to now have to go back to Brussels to ask for cash.
She said: "It's really great news that they are going to apply for this funding, it's one of the benefits of membership of the EU. I think delays have been because of the Government's nervous relationship with the EU at the moment. However this is money will go a long way towards helping rebuild Calderdale.
"We are all a bit baffled about why it's taken the Government so long. This is a U-turn as the Prime Minister ruled this out and James Wharton indicated for the first time recently that the Government were thinking about, and it's taken an urgent question from the Labour Party three days before the deadline to get clear clarification."
Mr Cunningham said the Government's failure to apply for the fund would have set people back from getting their lives back on track across the North of England.
The UK has paid £300m into it since it was set up in 2002, however the British Government has only once drawn on the money available to cope with the aftermath of the 2007 Oxfordshire floods.
The Government had 12 weeks to apply for the money following a natural disaster, and the deadline passes this Sunday.
Accountancy firm KPMG has estimated the total cost of the flood damage at £5bn, which means that the UK could be eligible for up to £125 million of, of which 10% would be made available immediately.
Liberal Democrat leader Tim Farron, whose Cumbrian constituency of Westmorland and Lonsdale was severely affected by this winter's floods, said: "Since day one I have called on the government to apply for this funding to help the North and parts of Scotland get back on their feet.
"It is an utter farce that it took the government until the eleventh hour, when we were about to lose this vital cash, for them to finally decide to send a letter and ask for the £125 million.
“Local people have shown overwhelming support in favour of applying for this money, and I am glad that the government has finally listened.
“Having to drag James Wharton, the Brexiter, to the Commons to announce that the government will apply for EU funding, and that it will really make a difference to our communities, was a nice final touch of irony.”
The announcement comes as RSA Insurance said the damage caused by a series of storms that raged across the UK in December 2015 has cost it £76 million.
The insurance group said flooding and other weather-related losses caused by storms Eva, Desmond and Frank ranging from Lancashire to central Scotland were "worse than planned".