The upgrading of President Jacob Zuma's Nkandla residence is riddled with anomalies, Public Works Deputy Minister Jeremy Cronin conceded on Tuesday.

"We have produced a preliminary report indicating that there are indeed serious anomalies, and strong indications that there has been over-charging, variations in cost," Cronin told the National Assembly.

"The difficulty is that you cannot make sense, that we cannot make sense of our report... unless you also look at the scope of the work: why were particular things ordered in terms of the security requirements?"

Cronin denied opposition claims that government was trying to cover-up a report pointing to these.

He defended a decision to table the findings of an internal investigation on Nkandla before Parliament's joint standing committee on intelligence – which meets behind closed doors – and said it was done on the "wise and correct" advice of Speaker Max Sisulu.

It was not problematic to disclose aspects relating to public works' role in the controversial R206-million upgrade, said Cronin.

However, security considerations underpinning the work could be heard only in closed committee.

"We want this Parliament, as a multi-party institution, to be able to have full scope, without any hindrance, but of course therefore in camera, because we are dealing with security matters and sensitive matters. We are not trying to cover up."

Cronin's statement was met with jeers from the opposition.

He was responding to a statement by Democratic Alliance parliamentary leader Lindiwe Mazibuko, who said Public Works Minister Thulas Nxesi had "classified" the report.

She challenged Nxesi to state, within a day-and-a-half, his reasons for keeping the report under wraps, and the official process he had relied on to do so.

Mazibuko said she believed the true reason was "to cover up the events surrounding the scandal to protect those at the top".

On Monday, Mazibuko said a state law adviser had told Sisulu the report was classified, and therefore his office had referred it to a closed committee.