Councillors on the region’s flood and coastal defence committee voted to raise local authority contributions by 14 per cent to plug a gap left by the loss of Yorkshire Forward match-funding.
It was agreed more money must be spent in 2013-14 to protect homes and businesses after this year’s record rainfall.
Committee chairman and North Yorkshire county councillor Arthur Barker said: “In times of extreme difficulty, this sends a message that authorities in this region are taking it very seriously.”
Local authorities contributed a total of £1.75m to flood alleviation works across Yorkshire last year and £1.5m the year before.
The regional development agency had put forward £500,000 annually before it was wound up.
Sheffield councillor Jack Scott said raising the levy represented value for money for councillors.
“Good flood defences cost money but bad flood defences cost even more money,” said Coun Scott (Lab, Arbourthorne). “To not replace that Yorkshire Forward money would be an entirely false economy.
“If you look at the 2007 floods they put such a huge impact on us as a council – but also on our city.
“You can’t penny-pinch when it comes to saving lives.”
The local levy programme has traditionally been used to fund small-scale projects that were not eligible for flood defence grants-in-aid from Defra.
Now it is also an important source of top-up funding after the grants were made available to a wider range of projects under a new partnership funding scheme.
Projects are scored based on their flood-risk benefits and those that do not meet the funding threshold can seek to meet it by reducing costs or securing outside contributions – including from the levy programme.
It is hoped the extra £250,000 available in 2013-14 from councils in Yorkshire and neighbouring counties will help to attract more public and private sector funding towards regional flood defences.
The amount to be paid by each council now equates to £1.28 per Band D property, up from £1.11 this year. It is still among one of the lowest rates in the country.
The change will not result in a council tax rise. Local authorities said they had included the rise in next year’s budget projections but most had yet to fix on where savings will be made to allow for it.
A spokeswoman for North Yorkshire County Council, which faced a £1.8m bill from September’s floods, said every spending increase was difficult when it was tasked with saving £91m.
But she added: “Flooding prevention is a critical issue for us so we believe that meeting this extra cost is necessary.”
The rise has also been hailed as a necessity in Calderdale, where 800 homes and businesses were flooded in June.
Barry Collins, cabinet member economy and environment, said: “For Calderdale, this year’s floods were a dreadful warning. Despite the spending cuts we face, it therefore seems right to increase the council’s levy contribution.”