In March, the Health Secretary Jeremy Hunt banned the use of gagging clauses in compromise agreements.
The move followed calls for a culture of "openness and transparency" in the NHS after the Mid Staffordshire scandal in which as many as 1,200 patients are thought to have died.
However a Freedom of Information Act request has today revealed that hospitals have spent £2 million on top of the £15m on more than 50 gagging orders.
But the government says that the March figures did not include "judicially mediated" settlements, meaning that the Government had no chance to block them.
The Department of Health said the system had been changed so that all severance payments were properly scrutinised.
A 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.
"Judicial mediation payments cannot prevent staff from speaking out about matters on patient safety or in the public interest."