Public Works Deputy Minister Jeremy Cronin criticised the National Key Points Act in a written speech but failed to mention it during the State of the Nation debate, it was reported on Friday.
The Cape Times reported that in the speech for the debate this week, he had referred to the act as "dastardly apartheid legislation".
He said that although the act was still in force and relied on by the government for some matters, it was "awkward" legislation and Parliament needed to "evaluate if that's what we want in the new South Africa".
The apartheid-era act applies to any place or area so important that its loss, damage, disruption or immobilisation may "prejudice the Republic".
It also applies whenever a minister of police or defence considers it necessary for the safety of the Republic or in the public interest.
The act was cited by Cronin's immediate boss, Minister Thulas Nxesi, when he refused to make public the full report on a departmental investigation into the R206-million security upgrade at President Jacob Zuma's Nkandla home.
According to the report, Cronin omitted any reference to the act during the debate.
He defended himself on Thursday, saying he had not had time to read his entire prepared speech.
He later said that while he felt the legislation should be changed, there should still be guidelines concerning sensitive information about Zuma and other officials' security.