The number of acute and specialist foundation trusts that missed cancer treatment targets rose by a third to 28 out of 90 in the past three months, their regulator Monitor has revealed.

Monitor’s report on foundation trust performance during the second quarter of the financial year states that cancer targets “continue to present the most significant challenge for foundation trusts”.

Seven foundation trusts also told the regulator they were at risk of breaching MRSA targets in July to September, compared with just two in the same period last year.

The report said this was “possibly due to more challenging national targets applied to all NHS trusts and foundation trusts”.

But the number of trusts reporting at risk of breaching C. difficile targets fell from 13 to 12 during quarter two.

The report shows that 62 per cent of foundation trusts (including 40 mental health organisations) are behind on delivering their cost improvement plans. However, the extent to which they were behind improved from 17 per cent behind plan in quarter one to 11 per cent.

Twelve trusts had yet to sign at least one of their contracts for the year, and a further 24 reported potential disputes over signed contracts, typically concerning “non-payment for over-performance”.

The report notes that “as contract disputes generally emerge at year end we would expect these to become an increasingly significant factor in quarters three and four and this could cause financial uncertainty at a number of trusts”.

The number of foundation trusts with red ratings for governance fell from 13 in the first quarter to 11.

The report said the “marginal tariff for emergency activity”, under which hospitals are paid just 30 per cent of normal rates for emergency work they do above planned levels, had not yet affected their financial risk ratings.