Briefing the media at Parliament on Thursday, he said the "disorderly and chaotic" sitting of the House last Tuesday had embarrassed all MPs.
"The chaos and disorder in the NA on Tuesday, which included the banging of tables, notably by DA MPs, in full view of the public, represented one of the lowest points in the history of our multi-party debates."
Motshekga was referring to what happened during the sitting on that day when he moved a motion that Congress of the People leader Mosiuoa Lekota be censured for "misleading Parliament".
Opposition MPs, including DA members, shouted, booed and banged on their desks while Motshekga was speaking.
Earlier, Lekota had been ordered out of the House - by Deputy Speaker Nomaindia Mfeketo - for refusing to withdraw a statement he had made a week earlier, in which he said that President Jacob Zuma has "defied" a court order.
He said at that time that Zuma had "defied an order, by the Supreme Court of Appeal, to hand over the abbreviated transcripts of the tapes that permitted criminal charges to be dropped or withdrawn against himself".
On Thursday, Motshekga said MPs' conduct had been shameful.
"There is absolutely no justification for the abhorrent behaviour, regardless of how aggrieved some MPs were with the decision of the presiding officer.
"Such unbecoming conduct is unacceptable and severely damages the trust, respect and confidence the public should have in this Parliament," he said.
Motshekga said a meeting of the multi-party chief whips' forum on Wednesday had "reflected at length on the matter".
"All parties agreed to work both jointly and individually to maintain order and respect for House proceedings, and defend the integrity of Parliament."
An appeal had been made to all parties at the meeting to respect the rules of Parliament and uphold the decorum of the House.
Motshekga "rejected the charge levelled at the ANC that it is stifling freedom of expression in Parliament".
On Lekota's statement, he said an allegation of "violation of oath of office" or "defiance of a judicial order" by a head of state was a serious matter.
MPs who wished to bring such allegations of improper conduct should do so, in terms of Parliament's established practice and procedures, by way of a substantive motion.
"The claim that some opposition MPs get kicked out of the House for criticising the president is inaccurate and deliberately misleading," he said.
Speaking at the briefing, John Jeffrey, parliamentary counsel for the deputy president, said the notice of motion to have Lekota censured was based on his "deliberately misleading" the House.
"What he said was not correct," Jeffrey said.
Parliament has yet to place the matter on its programme.