Makasembo said if Kindiki does not have faith in the Kenyan judiciary, then he should move the case to the United Nations International Court of Justice.
"As lawyers representing Makenzi, we will also boycott court proceedings and hearings until we get an assurance that there will be no interference with the courts during the trial of our client. We want an assurance of the court's independence," he said.
He said further: "We want an assurance from the Chief Justice of the court's independence in the trial of pastor Makenzi's case following the statement by CS Kindiki that our client will rot in jail regardless of the court's decision."
Mr Shikanda, however, said Kindiki's remarks would not influence the decision of the court. "Courts are independent and free from any external influence."
"I have heard and noted the concerns of the parties. It is obvious the remarks made were not for this court. The remarks were by the Executive arm of the government and they belong to it. The Judiciary makes decisions independently. Hence I will not speak for the CS on this matter since this is not the right forum for me to do so," said Shikanda.
He added: "I however know the impact of the statement on the suspects. They are apprehensive because they feel they may not get justice. However, they should have faith in the court since I will be guided by evidence and materials tabled before the court."
On Sunday, Kindiki said even if the court sets Makenzi free, he will still be returned to prison and stay in jail until his death, and also face judgment in the afterlife.
"Makenzi will not get out of jail. He will age in there. We pray that God gives him more years to see Kenya's security prosper. He will not get out of jail. Makenzi will meet the wrath of God after jail," said Kindiki.
Makenzi is accused of luring his followers to death through starvation and dehydration, in the name of religion.
Some of the dead children were strangled, while others were attacked by blunt objects, according to the autopsy.
On June 2, Makenzi protested his "perpetual detention" and asked the state to either charge or release him on bail.
This was after the Senior State prosecutors Jami Yemina and Peris Bosibori sought an extra 60 days to detain him pending the conclusion of investigations.
Makenzi's other lawyer Elisha Komora said if the State has evidence linking his client to the alleged massacre in Shakahola forest, they should charge him together with the co-accused.
The State claims Makenzi ordered the followers of his church to fast until they meet Jesus Christ and ostensibly attain martyrdom, a claim Makenzi has denied.
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All this time, Makenzi is said to have been eating well, promising his followers that after he has overseen their fasting and attainment of martyrdom, he will follow suit, and also fast to death.