A dozen hospitals are "significantly underperforming" basic safety measures despite nine of them being rated good or excellent by the official health regulator, a report said today, sparking a fierce argument over the accuracy of inspection regimes.

The latest Hospital Guide from the Dr Foster organisation also identified 27 trusts with unusually high mortality rates - totalling 5,000 more deaths than expected.

Of the 12 worst performing trusts in the new league table, nine were recently judged by the Care Quality Commission watchdog to be good or excellent.

Among those rated good was Basildon and Thurrock University Hospitals NHS Foundation Trust, which last week had a task force ordered in to sort out a series of failings.

Monitor, the body which regulates foundation trusts, stepped in after a report slammed poor hygiene and standards of care and a death rate around a third higher than the national average.

The Conservatives today called for a "massive overhaul" of the inspection regime, saying the data highlighted an "extraordinary contrast" between the Dr Foster and "box ticking" official assessments.

Shadow health minister Stephen O'Brien said: "Clearly there needs to be a massive overhaul in the way that the inspection regime is working.

"The failed system of self assessment can't carry on and we need to rip up the performance indicators - above all stop the tick-box targets."

The head of the Care Quality Commission, Baroness Young, said some of the part NHS, part private Dr Foster data was "very legitimate" while some was "quite alarmist".

"Where they are good we will take them to account in our regulatory work and where they are flaky, we won't," she said. "We do a comprehensive programme of monitoring, on a much more detailed level."

Baroness Young has said she does not believe any other trusts are performing badly enough to merit another task force-style response seen in Basildon.

The other 11 trusts ranked lowest by Dr Foster were University Hospitals Coventry and Warwickshire; Weston Area Health Trust; South London Healthcare Trust; Tameside Hospital Foundation Trust; University Hospital of South Manchester and St Helens and Knowsley Hospitals Trust; Mid Yorkshire Hospitals Trust; Blackpool, Fylde and Wyre Hospitals Foundation Trust; and Hereford Hospitals Trust are also among the 12, which are completed by Basildon and Thurrock; Lewisham; and Scarborough and North East Yorkshire.

Of these, St Helens and Knowsley was rated excellent by the CQC and three others - Mid Yorkshire, Weston and Scarborough and North East Yorkshire - were rated fair. The remainder achieved good ratings.

The Dr Foster research also uncovered widespread safety issues including 39% of trusts "failing to investigate unexpected deaths or cases of serious harm on their wards".

Items such as swabs and drill bits were left inside patients after surgery in at least 209 cases and surgeons operated on the wrong part of a body at least 82 times.

A total of 478 operations were also cancelled in 2008/09 because patient notes were missing.

And 848 of 5,024 people who died after being admitted for "low-risk" conditions were under 65.

Roger Taylor, the director of Dr Foster, defended his guide and said more information about trusts should be made public.

He said: "No hospital in the world would claim to be free of these kinds of errors.

"But what has been learned over the years is that recording what is happening, and making that information generally public, is the best way to start tackling the issues."

The day after the failures at Basildon emerged last week, the chairman of Colchester Hospital University NHS Foundation Trust was removed following concerns about high death rates, leadership and waiting times.

Health Secretary Andy Burnham ordered an urgent review by regulators to find out whether any other trusts required "immediate investigation".

The CQC said it was monitoring a small number of hospitals, but had "no evidence that there is another trust in England where we would take action of the kind we have taken at Basildon".

A Department for Health spokesman said: "Patient safety is absolutely paramount and it must be the highest priority for everyone in the NHS."

He went on: "The CQC will keep the situation under close review and to report back to the Health Secretary with any further concerns.

"We have made real improvements in recent years and England is recognised as one of the world leaders in the international drive to improve the safety of healthcare.

"The vast majority of patients experience high quality, safe and effective care and the CQC's recent survey showed that 93% of patients rate their overall care as good or excellent."

It was discovered earlier this year that between 400 and 1,200 more people died than would have been expected in a three-year period at Stafford Hospital from 2005 to 2008.