The Department of Education and Training spent $24.1 million on a new IT system that was scrapped before it was finished.
Department Secretary Michele Bruniges expect "not much" can be salvaged from the project, which was first funded in 2012.
At least two senior officials have left the department over the bungle, but Dr Bruniges told a Senate hearing on Thursday she remained behind to "take full responsibility".
"I have recognised and I have apologised publicly about the role in which the department's poor contract management played in this outcome," she told the committee.
The department is now expecting to spend up to $450,000 a year hiring staff to able to upgrade the dated original system, on top of an overall upgrade cost up to $900,000.
"What an absolute joke," Labor senator Doug Cameron said.
Education Minister Simon Birmingham admitted the implementation of the program was a "failure" and the outcome was unacceptable.
Of the total spent, NEC was given $10.5 million of an $11.7 million contract for the system, which was intended to track apprentices and tradies in training.
"So NEC got $10.5 million and delivered nothing?" Senator Cameron questioned officials.
The department's chief financial officer Marcus Markovic admitted that was the case.
Dr Bruniges said she made the final decision to scrap the project after three failed go-live attempts and based on advice from users that it wasn't meeting their purpose.
Department deputy secretary Subho Banerjee and skills program manager Brendan Morling have both left the department over the bungled contract.
Dr Bruniges said she had a conversation with Dr Banerjee regarding "his accountability and his responsibility for the outcome", but denied she pressured him to leave.