Staithes, known as "Britain's worst beach", and Saltburn, both in North Yorkshire, have failed to meet the minimum European standards for water quality – while 98 per cent of the country's beaches passed.
The other beaches that failed to make the grade are Heysham Half Moon Bay and St Annes in Lancashire; Walney Sandy Gap in Cumbria; Seaton, Instow and Mothecombe in Devon; Seaton in Cornwall and Lyme Regis Church Beach in Dorset.
Data published by the Department for Environment, Food and Rural Affairs (Defra) has revealed that just 10 of the 493 beaches and bathing spots monitored failed to meet minimum standards, compared to seven out of 495 tested last year.
The figures show that 86.2 per cent of bathing waters met the higher "guideline" standards set down by the European Commission (EC) this year, a rise from 80.2 per cent last year and a huge increase from 1990 figures, when less than a third of bathing sites made the grade.
Some 98 per cent of beaches and inland swimming areas met the mandatory minimum EC standards for water quality, down 0.6 per cent on last year's level. Those good results in 2009 came after two years in which heavy rain and flooding caused water quality to drop as pollutants were washed into the seas.
This year some 425 beaches and swimming sites met the higher EC standard. All 79 monitored beaches in Wales met the minimum standards, with 88.8 per cent reaching the higher "guideline" levels, while in England 97.6 per cent of bathing spots met the mandatory standard and 85.7 per cent reached the more stringent level.
Tougher standards are set to come into force from 2015, but already more than 80 per cent of beaches in England and Wales are clean enough to meet the new measures, the Environment Agency said.
The agency's chief executive Paul Leinster said: "The number of bathing waters in England and Wales attaining the highest quality status has almost tripled over the last 20 years – over eight in 10 sites now meet the EU guideline standard for water quality.
"The Environment Agency is working hard with others to drive improvements and tackle all sources of pollution alongside beach users, local authorities, farmers, land managers and water companies.
This news comes just a fortnight after it was revealed that Staithes and Saltburn are set to be among the smaller seaside resorts in Yorkshire that could miss out on a 110m package intended to turn the region's beaches into the best in Europe.
Earlier this month, Yorkshire Water and other public bodies announced a five-year vision for Scarborough, Filey and Bridlington which would smash water quality targets by improving sewage treatment and waste water storage.
However, all of the other seaside resorts – including Staithes and Whitby – were lumped together as areas where "Yorkshire Water's assets are not believed to impact on water quality.
Euro MP Tim Kirkhope, leader of the Conservatives in the European Parliament, has been fighting for a clean-up at Staithes for five years. He said: "These grand plans are fine. But you can't just include selectively two or three places and dump all the rest.
"Research is all very well. But in the meantime it runs the risk of Staithes being undesignated as a bathing beach and that would be a disaster as far as I am concerned because it is so important for Yorkshire tourism.
"Putting money into Scarborough is all very well. But Whitby needs money too if it to benefit from the enormous wealth which could be coming its way from the offshore wind industry.
The investment package is designed to ensure Yorkshire can fly all its Blue Flags despite the new European standards that will come into force in 2015.
Chief executive of Welcome to Yorkshire Gary Verity said: "Our aspiration is to see Blue Flags flying along our entire coastline.
"This would give us a higher concentration of Blue Flags than the likes of Portugal, a country widely regarded as having some of the finest beaches and bathing waters in Europe."