The former boss of the Rural Payments Agency has apologised "unreservedly" for its failure to pay out EU subsidies to thousands of farmers on time.
Delays to the 2005 payments also affected the 2006 timetable
Johnston McNeill told MPs, in a special secret committee session, the scale of problems with the computer system only became apparent at the last minute.
But he said he had had doubts about introducing a new payment and computer system while staff numbers were cut.
He appeared in private after failing to attend other meetings, citing "stress".
The RPA, a government agency, was charged with allocating about £1.5bn under the EU's single farm payment scheme (SPS).
The money should have been paid out by February last year, but that deadline was missed - slipping back to June - and more than 500 farmers were still owed money in December.
Many farmers claim the long delays in pay-outs have driven them to despair and even bankruptcy.
Mr McNeill was effectively suspended on paid leave in March and his employment terminated in December.
On Monday, chairman of the Environment, Food and Rural Affairs Committee Michael Jack told him the late payment of the Single Farm Payment Scheme cost farmers about £21m and "considerable stress".
It also had caused Defra to go over budget - resulting in cutbacks - and had disrupted the rural economy.
Mr McNeill replied: "I deeply regret that we in the RPA and I as chief executive were not able to make payments to farmers in the targeted timetable". He said he was "saddened by the consequences".
The RPA had been charged with introducing the subsidy - a major change to the way farmers received EU payments - as well as a new centralised computer system to process applications, at the same time as staff numbers were being reduced.
Mr McNeill said he recognised the job was "very high risk" from the start and had not wanted to apply, but was persuaded to by consultants.
Mr McNeill said the computer system, which hoped to rely on farmers going online, had become "gummed up".
As it was new, they were not able to properly test it as a whole and the scale of the problems with final security checks only became apparent at the "fifty ninth minute of the eleventh hour". Even then they came as a "very serious shock".
The change in the application process for subsidies came as a "culture shock" for farmers and a customer service centre was set up to help, but staff were not experts and were working off a "question and answer" brief.
Asked about the "mounting tide of complexity" he had to deal with, Mr McNeill told MPs the RPA had never said "this can't be done".
But he said his colleagues had repeatedly warned Defra that it was "high risk", and only became more so due to policy changes, delays and uncertainty about the payment scheme.
And asked why he had not told ministers it might prove too much to complete all projects to timetable, he said once notified in summer 2004 that the subsidy payments would begin in 2005 there was "no turning back".
He added: "We were an executive agency and we were there to do what the department wanted."
Speaking to the BBC later, committee chairman Mr Jack said it was to Mr McNeill's credit that he had apologised unreservedly.
He added: "But it does become apparent that other people had a finger in this pie and therefore should accept some degree of responsibility for what has occurred."
Most House of Commons committee meetings are held in public - and even those closed to the public and press are normally listed - but this session was not listed to take place, and only announced after it happened.
Mr Jack began the meeting by referring to a deal he had agreed with Mr McNeill to keep "the media hordes" away from the meeting.
A transcript of the meeting was placed, unadvertised, on the committee's section of the Parliament website on Wednesday morning.