Just over 1% of government infrastructure spending in England will go towards flood defences, analysis by BBC News has found.
Current figures show nearly £5bn is due to be spent on flood defences up until 2026, with a third of the money spent in London and the South East.
MPs in northern England said flood defence funding needed reallocating.
The government said it was investing "record" amounts in new flood defences that would protect 300,000 homes.
And it said in terms of money spent per home at risk of flooding, the North received more than the South.
Large parts of the country were battered last weekend by Storm Ciara, which resulted in more than 500 homes being flooded in Cumbria, Yorkshire and Lancashire.
Storm Dennis is bringing further disruption with dozens of flood warnings in place across England.
The Army was deployed to Ilkley and Calderdale in West Yorkshire to assist in flood relief efforts.
In York, the Environment Agency has predicted the River Ouse could reach record levels of 5.4m on Monday, a height not seen since 2000.
The Cumbrian town of Appleby-in-Westmorland was one of many rural towns affected by Storm Ciara's bad weather.
"Someone needs to stand up and be counted," said Dominic Boffin, as he swept flood water out of his home.
"We've had no help with the clean-up, and when it comes to the town being repeatedly flooded everyone seems to have their head in the sand."
Appleby was also badly affected in 2015 when Storm Desmond flooded more than 5,000 homes across the UK.
The then Prime Minister David Cameron said the flood defences in Cumbria "were not enough".
Appleby cafe owner James Brighurst said despite promises of new defences, none had materialised.
"We've seen a few subsidies for some individual buildings in the town but nothing has changed dramatically.
"There is a feeling we're being ignored and forgotten about".
The latest infrastructure spending figures published by the Treasury showed nearly £5bn was earmarked to be spent on flood defences in England over the next six years.
The money was due to be spent on more than 1,300 projects.
But flood defence spending makes up just 1.5% of the total £317bn set to be spent on all infrastructure across England, which includes upgrading roads and railway lines.
"Cumbria has had three 'one in 200-year' storm events in the last 10 years," said Tim Farron MP, Liberal Democrat spokesperson for Northern England, whose constituency is in the county.
"We know the climate is changing, and we also know that the climate is changing with the most impact here in the North West of England.
"So it is odd the government has chosen to spend so much money on London and the South East, and so little on the North.
"It's also staggering that we're spending so little money on flood defences altogether," added the Westmorland and Lonsdale MP.
York Central MP Rachel Maskell said the government had already failed to deliver on previous commitments made to upgrade flood defences in the historic cathedral city.
"Promises broken and programmes undelivered," said the Labour MP in the House of Commons.
"We have also seen a lack of delivery when it comes to issues like insurance and upper catchment management and even putting in extra flood resilience measures within the city."
Speaking before the government reshuffle on Thursday, the then Environment Secretary Theresa Villiers told MPs measures introduced by the government had protected 25,000 homes from being flooded by Storm Ciara.
"We are investing more than ever before in a £2.6bn flood defence programme up to 2021," she said.
"In the Autumn I announced an extra £60m to boost flood schemes in the North.
"Our manifesto commits us to an another £4bn of new flood defences funding up to 2026."
The Department for the Environment and Rural Affairs (Defra) said investment in flood defences took place where the risk was highest, wherever it was across the country, and each scheme was carefully considered.
"Funding is allocated consistently across the country, targeting national investment to reduce the risks of flooding and coastal erosion to as many people as possible and to get the best outcome for every pound we spend," a spokesperson said.
"We work with local partners to take into account local needs and opportunities when deciding where to invest."
Defra said its own figures showed that between 2015 and 2021, investment per home at risk of flooding was equivalent to £700 in the North, compared with £335 in the South.
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