Bernard Gray, chief of defence matériel at the MoD, said civil servants were told to calculate the cost of fitting a different plane to the massive vessels "by five o'clock" because they were wanted by some of "the most senior people in the country".
Coalition ministers ploughed ahead with the changes but were forced into a humiliating U-turn last year. The eventual reversal cost taxpayers at least £74 million, according to the spending watchdog the National Audit Office.
Mr Gray's comments come just days after MPs condemned the "deeply flawed" information on which the original 2010 Tory-LibDem Coalition decision was based.
"Incredibly basic errors" were made in the plan to install planes with so-called "cats and traps", catapult and arrester gear for landing and take-off, instead of the jump jets Labour had planned to buy, they found.
In evidence to MPs on the Commons Defence Select Committee, Mr Gray said that officials had been given an "absurdly short period of notice" to produce complicated technical costings.
He warned that for many civil servants "it is quite difficult to disagree with someone in the centre of the department who wants something to be true." Officials were often "put in an impossible position", he added.
The changes were made while Tory MP Liam Fox was the Defence Secretary.
Thomas Docherty, the Labour MP for Dunfermline and a member of the defence committee, said: "This is a shocking revelation about how last minute and rushed the decision on the aircraft carriers became.
"Nearly £100m of taxpayers' money was squandered on this half-baked scheme and the government must learn the lessons so that it never happens again."