The Foreign Office has said it "regrets" the time taken to establish the decision-making process behind the controversial evacuation of animal welfare charity staff from Afghanistan.
But it insisted information had been given to MPs in "good faith" and there had been no intention to mislead.
It conceded an "error" in communication had left some staff believing the prime minister made the decision to call Nowzad's staff forward for evacuation.
No 10 has denied any involvement.
However, in a report earlier this year, the foreign affairs committee said "multiple senior officials" believed Boris Johnson had intervened and "we have yet to be offered a plausible alternative explanation".
Its report stated that "after a mysterious intervention from elsewhere in government", Nowzad's workers had been called for evacuation "at the last minute", even though they did not meet the Foreign Office's prioritisation criteria.
The charity's animals were able to leave on a charter flight, which the MPs said had used "significant" resources.
The committee added that "under-resourcing of the evacuation effort in a crucial period likely cost hundreds of people their chance to leave the country, and as a result likely cost lives".
Nowzad was set up by former Royal Marine Paul "Pen" Farthing, who launched a high-profile campaign to get his staff and animals out of Kabul as the Taliban swept across Afghanistan in August 2021.
In response to the cross-party committee's accusation that its evidence had been "intentionally evasive, and often deliberately misleading", the Foreign Office acknowledged that "more care should have been taken" in how the "exceptional" decision was communicated to staff.
"The [Foreign Office] agrees with the committee on the importance of accurate record keeping, even in a complex, fast-moving crisis such as this," it said.
Labour MP Chris Bryant, a member of the committee, said the response failed to "clarify or explain the inconsistencies in their statements to the committee".
"So far we have had few signs that the foreign secretary and the Foreign Office are able to learn valuable lessons from this experience."
The Foreign Office also acknowledged the evacuation of people who did not qualify for the Afghan Relocations and Assistance Policy scheme had been "poorly communicated publicly and to Parliament".
Conservative MP Tom Tugendhat, who chairs the committee, welcomed the Foreign Office report.
"This disaster has exposed serious failings in the department and I hope that this response signals the start of a sincere attempt to remedy these failures," he said.