On The Runs: Record-keeping of cases criticised
The senior civil servant handling the On The Runs (OTRs) scheme for fugitive IRA members has said record-keeping was not good enough.
Sir Jonathan Phillips was permanent secretary at the Northern Ireland Office (NIO) from 2005 to 2010.
The NIO scheme saw 200 letters sent to OTRs assuring them they were not being pursued by the UK authorities.
In one case a man charged with the Hyde Park bombing walked free after he was wrongly told he was not wanted.
Sir Jonathan said: "I accept the criticism that in some cases the record-keeping... was not as good as it should have been.
"I am absolutely sure that it was not deliberate."
He said he worked with a group of officials in dealing with this and many other strands of the peace process, and added they displayed the highest level of integrity.
A judge-led review of the letters scheme ordered by Prime Minister David Cameron and published in the summer found it was systematically flawed in operation but not unlawful in principle.
However, Lady Justice Hallett, who conducted the probe, said a "catastrophic" error had been made in the case of John Downey, whose prosecution over the 1982 Hyde Park bombing was halted.
Sir Jonathan said: "I was disappointed by that criticism in the Hallett report but I did not take it as a criticism of the integrity of the officials, I took it as a criticism of the administrative efficiency of the office at a particular point."
He denied that anybody in the NIO altered any letters drafted by lawyers in consultation with criminal justice agencies.
Former senior police officers have said they were not aware of the exact wording of the letters.
Sir Jonathan told the Northern Ireland Affairs Committee of MPs: "It would have been much better from the outset of this process if it had been end-to-end and if the letters sent by the NIO had been copied to, amongst others, the PSNI (Police Service of Northern Ireland).
"The process would have been better had letters been copied from the NIO to a range of other parties who would have treated them with the degree of sensitivity which was required," he said.
He said the messages were not secret and no doubts surrounded the integrity of the police.
The committee launched an investigation after Downey walked free from the Old Bailey earlier this year.
His prosecution over the murders of four soldiers in the 1982 IRA Hyde Park bombing was halted by a judge after he received one of the letters in error.
Household Cavalry Lieutenant Anthony "Denis" Daly, 23, died in the explosion in Hyde Park on July 20 1982 alongside Trooper Simon Tipper, 19, Lance Corporal Jeffrey Young, 19, and 36-year-old Squadron Quartermaster Corporal Roy Bright.