NASA MCAs walked out in protest of Speaker Beatrice Elachi's refusal to allow them debate the People's Assembly motion.
The motion was not listed in the order paper but Minority Chief Whip Peter Imwatok wanted to use Standing order 51, which allows a member to issue notice and move a motion.
But Elachi decline this, saying the house had already gone past the "notice of motion" in the sequence of the order paper.
In response, Opposition ward representatives chanted "reject, resist" as they walked out of the chamber. They also accused Elachi of bias and favouritism.
Minority leader Elias Otieno accused Elachi of sabotaging the motion.
He told journalists the Speaker did not follow the sequence of the order paper and instead went straight to the last item - motion of adjournment - so as not to block the motion from being debated.
"This is a dictator speaker. We will bring this motion again next year in January," he said.
He said most of the Jubilee members were absent on Thursday, therefore the Speaker feared the motion would have gone through.
On Wednesday, the House business committee declined to allocate the motion time, citing a court order that barred assemblies from debating it.
Majority leader Abdi Guyo said: "We cannot allow the motion to be debated in our Assembly because it is illegal."
He said they would not entertain the motion that the court barred. He said he would write to CoB not approve to approve funds for counties that have passed the notion
Most recently, Kwale passed the People's Assembly motion despite it being led by a Jubilee governor.
Jubilee politicians in the region said they will go to court to challenge its passage and implementation.
NASA strategist David Ndii was arrested in Kwale and later released for his role in formation of the People's Assembly.
Mombasa MCAs passed the motion on Wednesday, saying President Uhuru Kenyatta is a "despot" who can no longer rule.