The Judicial Service Commission (JSC) has blamed the Attorney General for giving wrong advice on the appointment of judges.
This follows legal changes that have given the president more powers.
JSC had been named in the case filed by the Law Society of Kenya as a respondent, but it has switched sides and supported the case, arguing the president had no powers to reject or nominate a judge.
The commission, through lawyers Paul Muite and Issa Mansur, argued that the president's role was only to formalise the appointment process and not having the final say on who was to assume office as a judge or not.
In an opening statement, Muite claimed the squabble between the lawyers' body and the Government was as a result of Attorney General Githu Muigai's failure to give correct advice. "We are here because of their (AG's office) failure to give the correct advice," Muite told High Court judges Richard Mwongo, Mumbi Ngugi, George Odunga, Weldon Korir and Joseph Onguto.
READ MORE
Lawyers call for fresh vetting of judges to root out corruption
PS Omollo : We regret police action on femicide protesters
LSK criticises Uganda for blocking Karua from representing Besigye
JSC confirms five petitions filed against 10 judges over Sh3bn land case
Prof Githu through lawyer Mwangi Njoroge told the court that the judiciary could not be separated from the executive, as the President was the last resort in the process.
Last year, JSC had recommended 25 names to President Uhuru Kenyatta for appointment as High Court judges, but only 11 were confirmed.
This year, Parliament amended the JSC Act to have the president nominate a chief justice out of a list of three individuals forwarded to him by the commission. This is unlike the past where the president would endorse a single person.