The paediatric heart surgery unit at John Radcliffe Hospital in Oxford should remain closed until the right mix of doctors is in place or until it links up with another unit.
All four babies died within a few months of surgeon Caner Salih starting work at the hospital.
After the fourth death under his care, in February, he raised the alarm and decided to stop operating, having already complained about the age of equipment and poor working practices at the unit.
The investigation, by the South Central strategic health authority (SHA), said Mr Salih was not to blame for the deaths.
It pointed to issues within the Oxford Radcliffe Hospitals NHS Trust, including a lack of preparation for his arrival and no senior cover to help him.
When the doctor raised his concerns, the trust failed to act for at least 11 days and there was "no evidence" of a "clear plan of action".
Video: Hospital 'must not resume heart ops'
The report said: "On the contrary, there seems to us to have been attempts to minimise the scale of the problem and to restrict knowledge of it."
It was only when journalists began to investigate the incidents that the trust took action.
Today, SHA chairman, Dr Geoffrey Harris, apologised to the families of those babies who died.
"We offer our sincere condolences and we apologise that, in the cases, the standards of care were not what was expected," he said.
The investigation reviewed death rates and found that among 15 babies operated on by Mr Salih, the death rate was 4.8 times higher than would be expected from a national rate.
However, "all the cases were complex and surgery was high risk".
The report said: "In Mr Salih's four cases, we found no evidence of poor surgical practice, but that he would have benefited from help or mentoring by a more experienced surgeon."
It said it was "an error of judgment for him to undertake the fourth case" but the baby was so poorly it would have been very likely to die anyway.
The paediatric unit, which was temporarily suspended in March, is the smallest in England, carrying out just 120 or so operations a year.
Surgeons need a high enough caseload to maintain expertise but at Oxford there was a "fragile" situation, with just one surgeon handling the cases and leading a team with a low workload.
Furthermore, when less common procedures were carried out, the results were "significantly poorer than expected".
The panel noted that as soon as Mr Salih started work the unit's other surgeon, Professor Stephen Westaby, took holiday.
It was clear "the two had not satisfactorily discussed the matter" of what would happen during his absence.
The report added: "Mr Salih had insufficient time to familiarise himself with the unit's staff, facilities and equipment, all of which were geared to working with Professor Westaby."
He arrived from one of the world's leading heart centres and was used to new techniques but no preparation had been made to accommodate his preferences, the report said.
"The team had evidently grown accustomed to working with (Prof Westaby's) somewhat idiosyncratic approach.
"When the new surgeon was appointed, clear expectations were expressed that the two surgeons would work together and would participate in a single team, including operating jointly.
"This simply did not occur. It should have been clear from the outset that the two surgeons had significant differences of outlook and personality, and neither surgeon expressed any enthusiasm for joint working."
The report pointed to an "error of judgment" among the clinical team in deciding that Mr Salih, "as a new surgeon working with a team not yet used to his methods, should undertake some of these procedures without assistance from another consultant cardiac surgeon".
The report set out several recommendations, including an overhaul of the system for dealing with serious adverse incidents and better monitoring of death rates.
The panel "also recommends that paediatric cardiac surgery remain suspended in Oxford until or unless the service can safely be expanded".
The report added: "This might require some mix of both expanding the trust's service and forging robust links with another centre."
Oxford Radcliffe Hospitals NHS Trust is one of the largest NHS teaching trusts in the country and was given the top rating of "excellent" for quality of services in the 2008/09 by the Care Quality Commission (CQC).
Cynthia Bower, chief executive of the CQC, said it would conduct a full review of quality and safety standards across the hospital.
"While the report does not say that the failings caused any deaths, I am in no doubt that babies were not receiving care that was as safe as it should be.
"The trust did not handle the safety concerns raised by the surgeon in an effective or transparent way.
"The delay in notifying the board, strategic health authority and regulator was unacceptable.
"The clinical governance arrangements to identify and monitor safety risks were not up to scratch. Induction and supervision was clearly poor."
A statement from the trust said it was reviewing clinical governance and risk management processes, and acknowledged the "last few months have been very difficult for the families".
It added: "Children's heart surgery has been carried out at Oxford since 1986, with good outcomes.
"Professor Stephen Westaby has worked for a significant part of this time to provide the service on a daily basis, and he has rightly earned the trust and respect of patients, their families and the staff he works with."
Mr Salih now works at Guy's and St Thomas' NHS Foundation Trust, which said there was no need to restrict his practice.
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