The union has called on the County Assembly to enforce the Collective Bargaining Agreement (CBA) and Return to Work Formula (RTWF), mandate the redesignation of qualified doctors, settle outstanding arrears, and investigate employment terms that violate the constitution.
The Council of Governors will also initiate and coordinate the process of negotiating a new CBA with each county within 30 days.
The deal does not fulfil their demands regarding the matter of internship postings for medical graduates.
This follows several failed rounds of negotiations, which have seen the government unilaterally sign a return-to-work formula.
The Labour court has given doctors and the government another 48 hours to negotiate a deal.
Kenya is grappling with a significant healthcare crisis as workers continue to strike, demanding better working conditions.
The union is also accusing government officials of relying on "veiled threats and blackmail" rather than genuine dialogue.
CS Nakhumicha urges the KMPDU "to do the honourable thing and call off the strike that has, on several occasions, been declared illegal."
Prior discussions had reportedly resolved 17 out of 19 contentious issues, and this meeting aimed to find consensus on the remaining two.
President William Ruto asked doctors to end their strike as the government sought to meet their demands.
The Kenya Medical Practitioners Pharmacists and Dentists Union (KMPDU) underscored the enduring grievances against the government, which are yet to be resolved.
The healthcare system has long been overburdened and underfunded, but it has ground to a near halt after about 7,000 professionals walked off the job.
Only Kenya Medical Practitioners, Pharmacists, and Dentists Union (KMPDU) officials honoured the meeting.
According to the Head of Public Service Felix Koskei and Chairperson of the Council of Governors Anne Waiguru, 18 of the 19 issues the doctors wanted addressed have been solved except the issue of interns which is still contentious.
KMPDU Secretary-General Davji Atellah told the press that they must fight for interns, as they are the most vulnerable group in the profession.
Government officials say they are heading to court to seek clearance to have all the medics fired and replaced.
Doctors' representatives decline to attend meeting called by Head of Public Service Felix Koskei.
The KMPDC licensing committee has declined to clear four Ethiopian oncologists who have already reported to the hospital to replace the doctors who went on strike.