Sir Bob Kerslake said taxpayers' cash was only being released in stages as efforts continued to get Universal Credit on track.
The project to combine a series of welfare payments has been undermined by serious problems, especially with its IT elements.
Tens of millions of pounds has already been written off and the entire process "reset" so experts could be brought in to rescue it.
Sir Bob's frank admission came as Whitehall's most senior mandarins defended the speed of their intervention to deal with the issues.
He intervened after colleagues - including Treasury permanent secretary Sir Nicholas Macpherson -repeatedly dodged the question of whether it had now been signed off by officials when they appeared before a public spending watchdog.
"We shouldn't beat about the bush: it hasn't been signed off," he told the Commons Public Accounts Committee.
Universal Credit will replace jobseeker's allowance, income support, child tax credit and housing benefit, but its introduction has been slowed while the issues are worked on.