Up to 17 prisoners may have escaped from custody while private security firm Reliance was on duty, it has emerged.
Reliance has mistakenly released prisoners
The firm's managing director has been questioned by MSPs at the Scottish Parliament.
Tom Riall told the Justice 2 Committee that so far six of the releases can be blamed to some extent on Reliance.
Meanwhile, Justice Minister Cathy Jamieson has said she will stay in her job and complete justice reforms.
Reliance has been dogged by mistaken releases since taking up the contract for escorting prisoners.
Mr Riall told MSPs that the private firm had not anticipated the difficulties it would face when it took over the job of transporting prisoners to court.
But he insisted the firm was getting on top of the job and he expressed his hope that the Scottish Executive would lift the freeze it placed on the £126m contract.
"We do, however, deeply regret the early difficulties as we rolled out this large and complex contract," he said.
"There has inevitably been a learning curve, even for the most experienced of us.
"We are committed to delivering a quality service and we believe we are now achieving that."
Mr Riall said Reliance had not anticipated the complexity of the Scottish justice system, particularly in relation to warrants, and the unique nature of the Sheriff Court system.
He went on to explain that the firm was not given information held on the
Police National Computer (PNC) about outstanding warrants and suggested this
might explain why some prisoners had been released in error.
Ms Jamieson said she had been given a job to do and was doing it to the "best" of her ability.
She added that the roll out of the Reliance contract was still on hold and would
remain that way until the Scottish Prison Service (SPS) was convinced that the firm was ready to take on the task across Scotland.
She said: "SPS are answerable to me for that. SPS and Reliance are discussing
a revised implementation programme, no decisions have yet been taken and I can
assure you that Parliament will be informed when decisions are made."
During the evidence session, the minister repeated her view that the firm underestimated the job and its reputation had suffered as a result.
"But I think it would be quite wrong to paint a picture of a service that
continues to operate at the very poor level that was evident in the very early
days," she said.
Scottish Prison Service chief executive Tony Cameron also faced the committee.
A series of high-profile errors sparked calls for the publication of the Reliance contract.
Cathy Jamieson has come under pressure during the Reliance row
Information Commissioner Kevin Dunion ordered the executive to publish details after receiving a request for the information from the Scottish National Party.
Reliance was fined £75,000 for releasing three prisoners from custody.
Ms Jamieson has been supported by First Minister Jack McConnell, who said he believed Reliance had overcome its initial problems.
The justice minister has also come under pressure for failing to lodge an appeal over the slopping out compensation ruling.
The Scottish Executive ran out of time to appeal against a court ruling that slopping out in jails amounted to degrading treatment.
She said the error appeared to have occurred in offices which came under the auspices of Lord Advocate Colin Boyd.
Ministers have gone back to court to ask for more time to appeal against a judge's ruling that cells without toilets breach the human rights of inmates.