David Cameron has taken personal control of emergency efforts to help households stricken by floods and promised "no restrictions" on help, as Labour accused the government of leaving people isolated and unable to cope with homes under water.

The prime minister led a meeting of Cobra, the government crisis response committee, moving aside Owen Paterson, the environment secretary, amid criticism of the official response to weeks of flooding, power outages and transport chaos.

The Environment Agency now has nine severe flood warnings in place, covering much of the south coast from Cornwall to Dorset, as well as the Somerset Levels. A further 65 flood warnings are in place across southern England, the Midlands and Wales.

With more than 300 properties under water and 8,000 homes without power, the army has been drafted in to offer planning advice and stands ready to provide troops. Police have used megaphone warnings from a helicopter to urge residents in the flood-stricken Somerset Levels to leave their homes.

In Devon, a 30 metre stretch of the seawall in Dawlish has been swept away leaving the main south-west rail line dangling over the sea. Rail services west of Exeter are likely to face weeks of disruption and Exeter MP and former Labour environment minister Ben Bradshaw has called for the line to be rerouted.

The railway line is engulfed by waves in Dawlish, Devon. Photograph: Clive Postlethwaite/Rex

The Met Office and Environment Agency warned that the stormy weather is forecast to continue into the weekend bringing the risk of more flooding and winds bringing down trees and causing more disruption to travel and power networks.

After pledging an extra £100m for flood maintenance and repair, Cameron warned of more bad weather to come and said he would do "everything that can be done" to help those affected.

"My sympathy is with everyone affected by the ongoing storms which are causing misery to communities and businesses across the country," he said. "With power outages, more flooding and more bad weather forecast, I have chaired a Cobra this afternoon to ensure that everything that can be done to get stricken communities moving is being done: there are no restrictions on help."

He also promised a "proper alternative service" for rail travellers in the south-west after seeing "shocking" pictures of a train line that fell into the sea in Dawlish in Devon during the latest storms.

There have already been 21 emergency Cobra meetings of government departments, including representatives from the Environment Agency, Ministry of Defence and Met Office, to respond to the threat of floods since before Christmas.

Prince Charles in the flood-hit village of Muchelney in Somerset. Photograph: Getty

Cameron's greater involvement in the relief effort comes after the Prince of Wales called it a "tragedy" that some people had experienced delays in getting help.

"The tragedy is that nothing happened for so long. There is nothing like a jolly good disaster to get people to start doing something," Prince Charles said, as he visited some of the worst affected areas this week.

Despite the "serious situation", Cameron denied that the response so far had been inadequate or slow. He said "no amount of pumping will solve the current problem" completely because the land in the worst-hit Somerset Levels area is so saturated.

However, he admitted not enough had been done by the Environment Agency in recent years to dredge rivers in the south-west, where some parts have been flooded since Christmas.

Cameron also contradicted the claims of Lord Smith, the chairman of the Environment Agency, who has warned the body does not have enough resources to protect both the town and country.

Waves breaking over a jetty in Swanage, Dorset. Photograph: Paul Angel/Demotix/Corbis

The idea that only urban or rural areas could be defended from flooding was a "false choice", the prime minister said.

"From the late 1990s – far too long – the Environment Agency believed that it was wrong to dredge," he said. "I believe it is time for Natural England, the Environment Agency and the departments to sit round the table and work out a new approach that will make sure that something that did work, frankly, for decades and centuries is reintroduced again."

No 10 sources said the extra £100m for flooding repairs would be available over the next year and come from the contingency fund of the Department for Environment, Food and Rural Affairs (Defra), even though it is potentially earmarked for European Union repayments. The source said the EU would "have to wait" if the money was required.

There will also be changes to the emergency Bellwin fund, which is available to councils to claim back money spent on "emergency measures undertaken to safeguard life or property" during times of bad weather.

At the moment, local authorities can get 85% refunds on their costs, but now they will get 100% and have until March to make a request for flood aid.

Of the £100m, around £75m will be spent on repairs, £15m on maintenance and £10m on specific flood measures for the Somerset Levels. However, Friends of the Earth, the environmental campaigners, said this was "like trying to plug the leaks when the dam's about to burst", given the overall level of neglect in recent years.

Cameron defended the government against claims that spending on flood defences had fallen under the coalition, arguing more would be spent in the four years between 2011 and 2015 than in the previous four years under the Labour government.

However, a senior Labour sources said this was a "clear case of fiddling the figures", as Cameron included private sector spending in his calculations. In fact, government spending has fallen from £2.37bn to £2.34bn over those four-year periods. "They should stop playing with the statistics and get on with their job of helping those in need," the Labour source said.