Don't blame me for Home Affairs blunders, blame incompetent managers and low government salaries, the department's director general Mavuso Msimang told Sowetan.
Home Affairs was also the only national department to get a highly unfavourable audit opinion because it was unable to provide supporting documents for transactions worth millions of rand.
And on Friday, Msimang revealed that 70percent of senior managers had failed a competency test and would have to be persuaded to accept demotions or severance packages.
But he pleaded with the media not to use every blunder as "a stick to beat us with".
He said cases where people wait years for IDs, or men find they have been turned into women, are happening "less than 0,001 percent of the time now".
"In the past if you applied for an ID, 80 people handled your documents. There were opportunities for things to get lost or detached deliberately and put onto the document of someone else. We have reduced the number of people to 15," he said.
Msimang, who took over as DG a year ago, said he had known from the start that he was not going to be able to transform the department "with the same people who had been found to be not very efficient".
But former Public Service and Administration minister Geraldine Fraser-Moleketi prevented him from hiring people on market-related salaries.
The department has clashed with parliament's portfolio committee on home affairs, which instructed him to stop rolling out a new electronic ID system, after the auditor general said costs had spiraled from R1,8billion to more than R4billion.
But Msimang said "we can't stop it, we won't, unless we are ordered to and it would be a disaster if that were to happen".
He claimed that the auditor general had given parliament the wrong figure. "The auditor general made an apology to the portfolio committee for having misled them," he said.
But the DA's Mark Lowe said "Parliament has never seen any apology".
Lowe said: "The DA fully supports Msimang but how are we supposed to continue supporting him when he says the office of the auditor general apologised for releasing wrong figures? We have never seen evidence of this apology."
Msimang said people should stop calling for his boss Nosiviwe Mapisa-Nqakula to be fired.
"She inherited a department that already had serious problems, and had the courage to recognise that there were serious shortcomings," he said.