Published Friday, 07 March 2014
Ms Villiers has said the letters were not “get out of jail free cards”. (© Pacemaker)
Ms Villiers made the announcement during a speech to the Association of European Journalists in Belfast on Friday.
The move comes after the collapse of the trial of John Downey who denied charges of involvement in the 1982 London Hyde Park bombing.
Mr Downey was mistakenly informed by the PSNI in 2007 that there was no interest in him from them, or any other police force across the UK.
When the letter was revealed in court, the trial judge threw the case out ruling an abuse of process had occurred.
Ulster Unionist MLA Danny Kinahan has said he believes a second so-called "letter of comfort" has been sent to another individual also by mistake.
On Thursday, during a Policing Board meeting, the PSNI confirmed it checked 238 names for the scheme, with 192 found to be "not wanted".
Ms Villiers has now confirmed the scheme, which sparked a political crisis when First Minister Peter Robinson threatened to resign, is over.
She said anyone holding a letter should be aware that they are not "get out of jail free cards" or protect individuals from arrest or prosecution.
It needs to be clearly understood by all recipients that no letters which have been issued can be relied on to avoid questioning or prosecution for offences where information or evidence becomes available now or later.
"They were statements of fact at the time regarding an individual's status in connection with the police and prosecuting authorities," she said.
"No letters have been issued by the NIO since December 2012 and as far as this government is concerned, the scheme is over.
"If at any time we had been presented with a scheme that amounted to immunity, exemption or amnesty from prosecution implied or otherwise, we would have stopped it immediately."
Three inquiries are to be conducted into the OTR scheme.
Prime Minister David Cameron has ordered a judge-led inquiry. The Northern Ireland Affairs Select Committee will conduct its own probe and the Police Ombudsman is also investigating.
Meanwhile Ms Villiers said it is important for the Executive to agree an approach on the issues of the past, parades and flags which commands "public confidence".
She said the Executive needs to "move forward" and work on issues such as welfare reform and on tackling organised crime.
© UTV News