In recent years the department has become notorious for overspends and procurement problems. But Bernard Gray said that civil servants in his department had "their arms put up behind their backs" to produce hasty costings for projects.
Earlier this week Mr Gray revealed that in 2010, when Tory MP Liam Fox was Defence Secretary, officials were given just hours to estimate the cost of changing the planes to fly from the carriers.
Mistakes in that process led to a humiliating U-turn by Mr Fox's replacement Philip Hammond last year and have cost the taxpayer at least £74million.
Appearing before a separate committee of MPs, Mr Gray said officials should have been given six months, not a day, to complete the work. He said what was eventually provided was "opinion".
"People (within the MoD) come under pressure, with people saying, 'Everybody wants to know, we have to have an answer today,'" he said.
"'If you were any kind of a person you would be out there and would be able to tell us what this costs,' and so on and so forth; people have their arms put up behind their backs, and so they put in a number. That is a fundamental mistake and a weakness of the current system: it allows people to offer an opinion about something when they cannot about something like that." …
Instead, he told members of the Defence Reform Bill Committee, officials should have said that they could not offer costings without months of work "however much you want us to".
The MoD has stressed that Mr Gray has set out plans to change defence procurement to improve value for money for the taxpayer. A source suggested that by "opinion" Mr Gray was referring to estimates based on expert knowledge and provided due to time pressures.
But Thomas Docherty, the Labour MP for Dunfermline and a member of the Commons Defence Select Committee, said: "The Defence Review was a disaster that resulted in wasted money and a loss of vital defence capabilities."
Earlier this week MPs condemned the "deeply flawed" information on which the original 2010 decision was based.
"Incredibly basic errors" were made in plans to install aircraft with catapult and arrester gear for landing and take-off, instead of the jump jets planned under Labour, they found.
On Wednesday Mr Gray told MPs on the Defence Select Committee officials were asked to provide costings by "five o'clock" the same day.
Last year, the Commons public accounts committee (PAC) concluded that the taxpayer too often had to pick up the bill for the MoD underestimating the risks involved in building complex weapons systems.
It highlighted three large projects which suffered from long delays and overspend, including the Nimrod maritime patrol aircraft which was scrapped in a 2011 review to save costs, despite £3.4bn being spent on the project.
MPs on the PAC said it was unacceptable the department could not identify the size of the gap between resources and expenditure.