The number of NHS foundation trusts failing to meet the target for seeing patients within four hours of arriving at accident and emergency departments has doubled in the last year.

A quarterly report by regulator Monitor found 31 trusts missed the target in April-June, compared with 13 over the same period in 2012.

Labour seized on the figures to claim there would be “severe storms ahead” for A&E units this winter unless the government addressed issues in staffing and social care.

The regulator’s report said: “We are concerned about waiting times in A&E, which normally improve in the spring and early summer, but which this year remained challenging for 31 foundation trusts [that] failed the four-hour target in the quarter ended June 30, 2013.

“This compares to 13 in the same period last year. Long waits in A&E may result in patients experiencing unsatisfactory care and the persistence of problems means that it is essential for trusts to plan appropriately and have the right funding in place if the challenges of next winter are to be dealt with effectively.

“Monitor is working closely with the NHS Trust Development Authority and NHS England to ensure that trusts are planning effectively for this winter overseen by urgent care boards.”

The number of FTs running a financial deficit increased from 36 in the first quarter of 2012-13 to 48 for the equivalent period this year.

The overall deficit was £74m, although the regulator stressed that figure was mostly due to a small number of “particularly financially troubled trusts”, including Peterborough’s £40m annual gap.

During the first quarter of 2013-14, trusts generated £57m less in cost savings than originally planned. Monitor’s analysis suggested that increased demand for services forced trusts to curtail planned savings on pay and supplies.

But the regulator said that despite the shortfall on planned cost savings, financial performance was ahead of plan. The sector reported an overall surplus of £27m, partly because revenue was 9 per cent higher than expected due to increased demand for hospital services.

Jason Dorsett, Monitor’s financial risk and reporting director, said: “Our analysis of returns from foundation trusts shows that patients are still waiting too long at A&Es in a number of foundation trusts.

“Increased demand means more than ever that trusts need better and earlier planning to make sure they deal with these problems.

“The increased demand has also prevented trusts from delivering their planned financial savings. We expect to see trusts planning now for how the increased demand will impact on their finances, so that they are not storing up trouble for the future.”

Shadow health secretary Andy Burnham said: “This survey shows that the pressure is now being felt in all parts of the NHS, with even the highest performing organisations losing their grip on waiting times.

“A&E is the barometer of the whole of health and care. It is telling us that there are severe storms ahead for the NHS this winter unless the government urgently faces up to problems with front-line staffing and in social care.”