He said the order was specific that the assembly should not implement or constitute the People's Assembly but passing the motion was in order.
"This house cannot be barred from debating motions. We are not constituting the People's Assembly. We are simply passing the motion," said Mr Ngunga.
He said he was dismayed that the office of the clerk had not furnished the assembly with the legal opinion.
Mr Ngunga claimed that some 'Jubilee Party moles' in the assembly were frustrating debate on the motion. He was, however, forced to withdraw the term 'mole' as it was not parliamentary language.
But some members opposed the debating of the motion, saying an assembly whose role was to pass laws could not disobey a court order.
Muthwani MCA George King'ori (Jubilee Party) received a warning from Speaker Florence Mwangangi when he said: “This house cannot be led by goons.”
Ms Mwangangi dared him to repeat the remarks.
"What language did you use? I am going to take up the matter with you later," the Speaker told Mr King'ori.
Ms Mwangangi said the assembly would not curtail debate.