The talks centred on human resource standards and challenges in the way of the universal health coverage (UHC) mission.
The deal does not fulfil their demands regarding the matter of internship postings for medical graduates.
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.
KMPDU Secretary-General Atella early in the week affirmed the union's commitment to the strike until the government honours the CBA.
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.
According to those impacted, families are compelled to care for their loved ones at home following a 38-day strike because they cannot afford to pay for care in private clinics.
The government is seeking 30 more days for the negotiations, a period during which it wants doctors to provide minimum services.
The rights body is pushing for talks to end the strike and wants the immediate end of threats by the government.
They say they delayed their strike to keep from burdening the people during Ramadan.
KMPDU say they follow proper channels to ensure peaceful demonstrations but are met with threats of force and intimidation.
Police IG Koome said medics participating in the strike have become a public nuisance, using whistles and vuvuzelas during demonstrations.
Despite a plea from Head of Public Service Felix Koskei to halt their strike pending government engagement, the doctors remain steadfast in their resolve.
Besides resolution of the health crisis, Azimio leaders want farmers compensated following the fake fertiliser scandal, and the resignation of the Health and Agriculture CSs.