The study for regulator Monitor found delivery of cancer targets was a “key challenge” in 2010/11 and continued to be so for some trusts in the first quarter of this financial year.
Some 32 out of 137 foundation trusts reported they have failed to meet one or more cancer targets in the first quarter.
In the Greater Manchester and Cheshire Cancer Network, the Christie NHS Foundation Trust has “persistently failed” to meet the 62-day cancer waiting time target.
Overall, 29 trusts reported breaches of this target, which says patients urgently referred with a suspicion of cancer by their GP should wait a maximum of 62 days to start their first cancer treatment.
Seven trusts are at risk of being considered for “escalation” over cancer target failures. This means Monitor undergoes a process of assessing whether a trust is in significant breach of its terms.
Foundation trusts also told Monitor they were finding other targets difficult, including those to cut the bug Clostridium difficile (C diff), referral to treatment times and A&E waiting times.
Some 31 trusts reported a higher than predicted number of breaches on C diff, despite a drop in the bug’s prevalence overall, while eight have declared a breach of the new target for total time spent in A&E.
There were also 18 reported breaches of the 18-weeks referral to treatment waiting time for inpatients.
However, on finances, the report suggests the foundation trust sector is performing “slightly ahead of plan”.
Monitor’s chief operating officer Stephen Hay said: “It’s encouraging that the sector is in overall surplus and ahead of plan for the first quarter - although surpluses are lower than last year due to the economic environment.
“But there are a number of foundation trusts that are beginning to struggle and we are looking closely at these and taking regulatory action in several cases to make sure that the issues are addressed.”
Mr Hay said trusts in the Greater Manchester and Cheshire Cancer Network had been told the situation on cancer waiting was “unacceptable”.
He added: “Patients are not being treated as quickly as they should be.
“It’s the responsibility of all the trusts in the network to make sure that this changes, by improving referral times.
“We have written to all seven foundation trusts and made it clear that we will use our regulatory powers if they don’t find a way of delivering a solution.”
The number of trusts with outstanding compliance concerns or actions from the Care Quality Commission (CQC) is also currently 36, an increase from 25 in the previous report.
Mike Farrar, chief executive of the NHS Confederation, said: “This is further evidence that pressures are mounting across the NHS.
“By far the biggest problem the NHS is facing is the £20 billion of efficiency savings we need to find by 2015. This is a problem we cannot ignore.”