Hospitals will be fined £250 each day for each patient treated in mixed-sex accommodation, Ministers have warned.
Latest figures show 11,362 patients last month spent time in accommodation with shared sleeping, bathroom or toilet facilities in England, out of an estimated 1.4 million courses of treatment.
Health Secretary Andrew Lansley said the breaches were "unacceptable" and accused Labour of covering up the problem.
The Conservatives promised to build more than 40,000 single hospital rooms when they were in opposition but the pledge was abandoned when the huge costs became clear.
About half the hospitals said none of their patients were in mixed-sex wards. The biggest problem appears to be in the North West where there were 2,800 breaches of rules compared with 180 in Yorkshire, with the lowest rate.
Four hospital trusts in the region accounted for most breaches. Patients in Scarborough and Bridlington hospitals were most likely to be treated with members of the opposite sex, while there were also significant numbers at the Mid Yorkshire Trust, which runs hospitals in Dewsbury, Wakefield and Pontefract, and Rotherham. Three hospitals did not provide figures.
Mr Lansley said it was the first time the figures had been published.
"It exposes the scale of the problem, which is far worse than we were led to believe," he said.
"This Government is committed to sorting out the scandal of mixed-sex accommodation. Labour were only concerned about covering it up."
The fines will be enforced in April.
A Labour Party spokesman said: "Thanks to Labour's investment, by 2010 around 95 per cent of NHS trusts had virtually eliminated mixed-sex accommodation from hospitals across England – a huge improvement from the neglected NHS we inherited in 1997.
"In opposition, the Conservatives promised to build 45,000 new single rooms in the NHS, but they have dropped this commitment – yet another broken promise from David Cameron."