Chief Justice David Maraga is under siege after the Supreme Court quashed the re-election of President Kenyatta.
On Thursday, Nyeri Town MP Ngunjiri Wambugu filed a petition before the Judicial Service Commission seeking the removal of Kenya’s top judge.
In the 14-page petition, Mr Wambugu accuses the president of the top court in the land of “gross misconduct”.
The Jubilee lawmaker wants the Judicial Service Commission, the employer of judges and magistrates, to investigate the conduct of Judge Maraga since his appointment as Chief Justice.
Mr Wambugu accuses the CJ of instituting "a judicial coup" as the head of the third arm of government.
Wambugu claims Judge Maraga has been held captive by a group of NGOs who have been campaigning against Mr Kenyatta's presidency since 2013.
He alleges that Justice Maraga has allowed the non-profits to be embedded in the Judiciary and has been funding a number of programmes, including technical support and training at the Judicial Training Institute.
He has also accused the CJ of preventing Justice Mohamed Ibrahim from participating in the hearing of the presidential petition filed by Mr Odinga.
Justice Ibrahim fell sick on the second day of the hearing of the case.
The allegations come as Kenyans eagerly await the full judgement of the Supreme Court, which nullified the re-election of President Kenyatta. The Judges have nine days to deliver their decision in full.
Justice Maraga, Deputy Chief Justice Philomena Mwilu, Smokin Wanjala and Isaac Lenaola nullified the election citing irregularities and illegalities in the transmission of results.
Judges Njoki Ndung'u and JB Ojwang dissented.
The Constitution states that the Chief Justice can be removed from office only on the grounds of inability to perform duty due to mental or physical health, a breach of conduct, bankruptcy, incompetence or gross misconduct.
The removal, Article 168 of Constitution says, can be initiated only by the Judicial Service Commission acting on its own motion, or on the petition of any person to the commission.
The commission, if satisfied with the grounds raised in the petition, shall inform the President in writing, leading to the formation of a tribunal consisting of Speaker of the National Assembly, three superior court judges, an advocate and two other persons to investigate the judge.
The petition was also filed a day after Jubilee senators, in a House debate, planned a series of laws to trim powers of the Judiciary on elections.
President Kenyatta and his Deputy William Ruto, angered by the nullification of their re-election, vowed to deal with Justice Maraga and the courts in case they are re-elected on October 17.
Additional reporting by Silas Apollo.