The boss of NHS England has faced furious calls to quit after it was revealed hospitals have spent £2 million on more than 50 gagging orders preventing staff speaking out.
Tory MP Steve Barclay, who obtained the figures, accused NHS chief Sir David Nicholson of either failing to ask questions about the orders or being "complicit in a cover-up".
Northampton General Hospital paid £50,000 to silence a whistleblower in 2011 and £95,000 to another the following year.
The Royal United Hospital Bath NHS Trust paid £128,000 to four outgoing staff in 2010. Even children's hospital Great Ormond Street Hospital handed over £38,000 in exchange for gagging staff.
Sir David, who is paid £270,000 a year, will retire as NHS England's chief executive next year but Barclay said he should stand down now because the culture in the health service had to change.
The Daily Telegraph reported that at least 52 staff have been silenced using the orders since 2008, some of which cost as much as £500,000. All are thought to contain confidentiality clauses.
Barclay is a member of the influential Commons spending watchdog the Public Accounts Committee (PAC), which Sir David is due to appear in front of on Wednesday
In March, Health Secretary Jeremy Hunt banned the use of gagging clauses in compromise agreements after it emerged that NHS hospital trusts had spent £15 million on silencing almost 600 staff.
But those figures did not include "judicially mediated" settlements, under which a hospital reached an agreement with staff which was then signed off by a judge or senior lawyer rather than the Department of
Health or Treasury, meaning that the Government had no chance to block them.
North East Cambridgeshire MP Barclay told The Daily Telegraph: "It is simply not plausible that the man who was supposed to be running the NHS was seemingly unaware that employees threatening to speak out were being offered golden goodbyes in return for a vow of silence."
The newspaper reported that Sir David told MPs in March that he had only come across one of the orders.
But Barclay said: "As the accounting officer who has presided over this culture he is either complicit in a systemic cover-up or has failed to ask questions. If he knew about them he has misled Parliament.
"The culture in the NHS needs to change, he has to stand down now. What patient safety concerns have been covered up (by these gagging orders)? How many lives have been put at risk?"
A Department of Health spokesman said the system had been changed so that all severance payments were properly scrutinised and staff were made aware of their whistle-blowing rights.
The spokesman said:"Judicial mediation payments do not mean that someone is gagged - it is a way of resolving a dispute and suitable cases for this are decided on by a judge.
"The Department did not collect data on these payments prior to February 2013. This has now changed - all non-contractual severance payments, whether via judicial mediation or another means, need to be scrutinised by a national body and they will not be recommended for Treasury approval unless the NHS can show that they have made staff fully aware of their legal right to blow the whistle.
"Judicial mediation payments cannot prevent staff from speaking out about matters on patient safety or in the public interest - NHS staff are protected by the law, regardless of when their payment was made and whether or not it was via judicial payment or any other means.
"The Health Secretary has been absolutely clear that "gagging" is illegal and it will not be tolerated."
Sir David said that ''becoming the story'' after the publication of the Francis report into the Mid-Staffordshire NHS Foundation Trust scandal contributed to his decision to retire.
Campaigners called for the under-fire boss to be sacked after publication of the report into serious failings at the trust.
Sir David, who has worked in the health service for 35 years, was in charge of the regional health authority responsible for Stafford Hospital for a short period while patients were being mistreated.
Liberal Democrat health minister Norman Lamb said he "had a sense" that gagging orders were happening in the NHS, but added that he was horrified by them.
"I'm horrified at the idea that somebody can be silenced" he told Daybreak.
"I had a sense that it happens too much, but it shouldn't happen at all. It's scandalous.
"There must be a culture of openness ... not to keep people quiet."
He added that Sir David has to be answerable "for what he knew".