The Health Secretary Jeremy Hunt said Sir Roger Boyle would play no further part in a review of where children's heart surgery should in future be carried out.
The government's former heart tsar sparked controversy last week when he told the BBC he would not send his daughter for treatment at Leeds General Infirmary's child heart surgery unit.
Mr Hunt said that while Sir Roger was still one of the leading heart surgeons his role in the Safe and Sustainable process aimed at centralising children's heart surgery into specialist centres would end.
He said: "He did the right thing in informing Sir Bruce (Keogh, NHS England Medical Director) about his concerns over Leeds mortality data.
"However it is the view of Sir Bruce, with which I fully concur, his comments to the media on April 11 could be seen as pre-judging any future conclusions made by that review and so it is right he plays no further role in its deliberations."
NHS England has released a statement saying 'immediate safety concerns' at the Leeds Children's Heart Surgery Unit have been addressed.
Local MPs in Leeds have called for Sir Roger Boyle to leave his role on the children's heart surgery review:
Children's heart surgery at Leeds General Infirmary resumed today, less than two weeks after all operations were abruptly suspended.
Concern had been raised over figures showing a high death rate at the unit but that data was discredited.
Now children are being operated on once again, as Damon Green reports.
The CEO of the Leeds Teaching Hospital NHS Trust has spoken out to reassure families about the children's heart surgery unit's reputation.
A mother from Wakefield, West Yorkshire, has said she is "absolutely thrilled" that the children's heart unit at Leeds General Infirmary is set to reopen.
Jo Lancaster, whose six year old son Toby has undergone two operations on his heart at the unit, said she has never had any doubts about its safety.
Anne Keatley-Clarke, chief executive of the Children's Heart Federation, has said that families affected by the suspension of the children's heart unit at Leeds General Infirmary are "very worried".
Several MPs based in the Leeds area have welcomed the news that the children's heart unit at Leeds General Infirmary is set to reopen.
Roger Boyle, director of the National Institute for Cardiovascular Outcomes Research (NICOR), has told Radio 4's Today programme that the decision to restart the children's heart unit at Leeds General Infirmary needs to be investigated.
Parents have reacted positively to the news that the children's heart unit at Leeds General Infirmary is set to restart.
Jon Arnold, whose daughter Zoe underwent heart surgery at the unit in 2007, said: