The Council of Governors (CoG) has now confirmed that doctors will not receive any pay for the days they were on strike.
This is despite an order by President Uhuru Kenyatta that the medics be paid their dues in full for the 100 days they were on strike.
On Tuesday, CoG chairperson for health Jack Ranguma dismissed the directive, saying it was not official.
"As Council of Governors, we are steadfast that the doctors will not receive pay for the days they were not working," said Mr Ranguma.
He noted that one of the reasons the medics cannot be paid is because the three-month strike was illegal.