A contingency plan will be put in place to deal with chaotic disruptions to parliamentary proceedings, Defence Minister Nosiviwe Mapisa-Nqakula said on Tuesday.

"The JCPS cluster wants to make it clear that the authority of the state shall not be undermined, neither will the authority of Parliament be undermined," she told reporters at Parliament during a briefing by the justice, crime prevention and security cluster.

"Certain measures by the security cluster have been put in place with immediate effect to ensure that never occurs again."

She condemned the action of Economic Freedom Fighters' MPs who disrupted proceedings in the National Assembly on Thursday while President Jacob Zuma was answering questions.

Both Mapisa-Nqakula and Police Minister Nathi Nhleko would not be drawn on exactly what "extraordinary measures" would be put in place.

"I do not want to get into the specifics. One of the measures we are putting in place is an overall contingency kind of plan," said Nhleko.

"We'll also want to look at the whole aspect of coordination [with parliamentary structures]," he said.

Mapisa-Nqakula conceded police "went into a state of paralysis" after Thursday's developments. Nhleko added the situation was extraordinary and had never occurred in the post-apartheid Parliament's 20-year history.

"Nobody would have expected that," Nhleko said.

"It's like walking into a church and expecting a dance party."

Nhleko said police exercised "a lot of restraint" on Thursday after Speaker Baleka Mbete instructed EFF leader Julius Malema and his fellow MPs to leave the House.

Malema was not happy with how Zuma had answered questions on when he was going to repay part of the R246-million spent on security upgrades to his private Nkandla residence in KwaZulu-Natal.

Public Protector Thuli Madonsela had recommended in her report on Nkandla, titled "Secure in Comfort", that Zuma repay that part of the money not spent on security measures, like the swimming pool and cattle kraal, among others.

Zuma has been accused of delaying responding in Parliament to Madonsela's report after he said he would leave it to Nhleko to determine if he should repay any of the money.