The Council of Governors will not pay doctors for the days they did not work during the 100-day strike.
Doctors on Wednesday threatened industrial action if they are not be paid allowances for the three months they were not on duty.
KMPDU accused CoG of undermining the recently signed deal by denying them the allowances.
In a letter to CoG chair Peter Munya, the union said if the doctors will not be paid by April 3, its members will resume their strike until the demands are met.
The union also demanded that governors withdraw a reference letter and a circular Munya issued to pave the way for unconditional payment of their salaries withheld before and from December.
But Munya said the Return-to-Work Formula document they signed does not capture the matter of salary payments to doctors for the days they did not work.
"The RWTF provides that no party shall victimise the other. Subsequently, the government withdrew all the show-cause and dismissal letters," Munya said in a statement on Thursday.
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He said it will be fraudulent and unprocedural to pay doctors accumulated salaries of about Sh3.2 billion without any basis in law when they participated in meetings and signed the RTWF that removed the clause.
"Doctors went on an unprotected strike on December 5, 2016 as the Labour court had declared it illegal. Several initiatives aimed at getting the doctors to return to work did not bear fruits and the doctors knowingly continued with the unprotected strike.
"It is therefore dishonest that doctors should be demanding to be paid for work not done," the Meru governor said.
Munya said the move by the doctors union was taking the wrong turn after reaching an agreement with the government then resulting to re-opening the talks through the backdoor.
"It is unfortunate that the union has not so far engaged any of the County Governments to negotiate for recognition agreements which is a critical step towards the realisation of a CBA." Munya said.
"The doctor’s strike has caused pain, suffering and death and it is immoral for KMPDU to play Russian roulette with Kenyans. The Return-to-Work Formula is the deal they bargained for," he added.