Speaker Baleka Mbete on Tuesday warned the Economic Freedom Fighters (EFF) she would not tolerate "anarchy" in Parliament, but was promptly challenged by party Chief Whip Floyd Shivambu, who accused her of bias.

"A situation where rules were not observed would be tantamount to anarchy," Mbete told the National Assembly.

"I cannot but strongly condemn the disruption of the proceedings in the chamber," she added, after confirming that she would not call on the House to suspend 20 EFF MPs, but leave the matter to Parliament's powers and privileges committee.

Mbete on Monday abandoned her stated intention to proceed with this sanction against the EFF for disrupting presidential question time late last month.

The change of mind came after the party threatened to launch a legal challenge in the high court.

However, she said she wanted to remind MPs that "in terms of rule 52 she could have suspended the members concerned immediately.

"At the time, I opted for a lessor sanction which was to order the members to leave the House.

"As members will remember, the refusal of the members of the EFF to abide by the directions and rulings of the chair led to the early adjournment of proceedings and the question session was not completed."

As soon as she completed her statement Shivambu rose to object, ignoring Mbete's protestations that she had not intended to open the matter for debate.

"How is the committee going to investigate when you are making conclusive remarks in this House?" he asked.

Mbete asked him to desist, but he continued: "We don't agree with all those observations that you have made here. The majority are wrong."

The EFF returned to the question of Nkandla and Public Protector Thuli Madonsela's recommendation that President Jacob Zuma repay public funds spent on personal improvements at his private homestead.

In a motion, the party again condemned recent attacks by the ruling party on Madonsela. It said there were people who wanted their leaders to be untouchable and "scandals like Nkandla" to be ignored, because their political future depended on said leaders.

Before the House adjourned for the day, the EFF issued a statement rejecting Mbete's remarks to the Assembly and accused her of interfering with the committee's work.

"The Speaker's prejudices and conclusive accounts of what she thinks happened on the 21st of August 2014 will altogether compromise the objectivity of the powers and privileges committee."

The party said she had been forced to withdraw her threat of suspension because it was in breach of the Powers, Privileges and Immunities of Parliament and Provincial Legislatures Act. This stated that no member may be threatened or deprived of any benefit because of his conduct in Parliament.

Shivambu had made this point in a meeting of the committee on Monday. He also argued that the ANC – and Mbete as the ruling party's national chairwoman – could not be trusted to handle disciplinary proceedings against the party in an objective manner.

The point found support from other opposition parties. Committee chairperson Lemias Mashile agreed to appoint an initiator for the charges who was not an MP.

Mbete has asked the committee to probe the EFF's conduct as a matter of utmost urgency and to report back to her as soon as possible.

On Tuesday, she told the National Assembly the party's conduct was of a nature never seen before in the Chamber.

"The frustration of the business of this House to this extent is unprecedented in the history of this democratic Parliament."

She denied calling in public order police to remove EFF MPs from the chamber after they refused to leave, chanting "pay back the money" at Zuma, in reference to public funds spent on Nkandla.

Instead, she said she had acted within her rights by calling on security to help her after the EFF continued its protest in "complete and open defiance" of the chair.

She warned that such behaviour would not be tolerated again.