During the presidency budget vote debate last Wednesday, Lekota accused President Jacob Zuma of violating his oath of office.
Lekota said, among other things, the president had failed to uphold his constitutional obligation to protect the rights of artist Brett Murray, who depicted Zuma with his genitals exposed, and City Press editor Ferial Haffajee, who refused to remove an image of the painting from the newspaper's website.
At the time, Higher Education and Training Minister Blade Nzimande asked Deputy Speaker Nomaindia Mfeketo, who was in the chair, to rule whether Lekota could make such a "serious statement" about Zuma.
"If a member of this House can stand and make a serious statement that the president has violated his oath of office... Such a statement is a serious thing. Madam chair I ask you to rule," Nzimande said.
Mfeketo said the matter would be ruled on later.
On Tuesday, Mfeketo ruled that members could make such allegations of improper conduct only by way of a substantive motion and ordered Lekota to withdraw his remarks.
Lekota refused, saying his conscience would not allow him to withdraw.
He maintained he was exercising his constitutional right to freedom of speech in Parliament, accompanied by such privilege as enjoyed by MPs.
Mfeketo then ordered him to leave the chamber. As he left the House he was joined by a large number of Cope and Democratic Alliance MPs.
In a statement afterwards, ANC Chief Whip Mathole Motshekga welcomed Mfeketo's ruling.
"An allegation of violation of office by a head of state is a serious matter that cannot be made lightly or for mere political posturing, as Lekota has done," he said.
In terms of Parliament's established practice and procedures, an MP who wanted to bring allegations of improper conduct should do so by way of a substantive motion.
"Parliaments all over the world have in place rules, conventions, practices, and codes of conduct to which MPs must adhere in order to preserve decorum, respect, and prestige of the state's legislative organs."
The ruling by the deputy speaker would dissuade "opportunist" MPs from abusing freedom of speech and parliamentary privileges to impugn the integrity of others without following proper procedure, Motshekga said.
However, Lekota said the truth remained that in debate on the president's budget vote, where the president was present, members could assert, on the basis of argument, that the president had indeed violated his oath of office. It was then for the president to respond.
Zuma had opportunity to rebut this accusation and in no way did it merit the withdrawal of the point by Lekota on the basis of the ruling by the deputy speaker.
The ruling gave no cognisance to the nature and scope of the debate taking place and the fact that the member of the executive could be challenged to the extent that he was by Lekota.
"Cope believes the ruling party has made a miscalculation of gargantuan proportion in attempting to curtail criticism of the president in the House, where the president has equal standing with all other members," Lekota said.