Kirinyaga Governor Anne Waiguru cracked the whip on Friday by stopping, with immediate effect, the remittance of dues to the Kenya Medical Practitioners, Pharmacists and Dentists Union.
Ms Waiguru accused the union of sabotage and undermining her leadership by asking health workers to strike.
On Wednesday, four unions in Kirinyaga issued a seven-day notice for the strike, citing poor conditions at facilities including Kerugoya Hospital.
The four are KMPPDU; Kenya National Union of Nurses; Kenya National Union of Clinical Officers; and Kenya National Union of Medical Laboratory.
Ms Waiguru emphasised that her government will no longer deduct and remit dues from doctors pay to the union, as it is "sabotaging operations in the health sector".
"There is no way I can continue empowering the union which is fighting me for no good reason. The union should pursue its members and collect the dues without involving my government," she said.
The governor said she read politics in the health sector debate as KMPPDU continued attacking her government after Kerugoya referral hospital was cleaned.
She said the health sector had improved in terms of cleanliness so the medics should ignore the call to boycott work and continue serving the people.
Ms Waiguru went on to say that the union misled members and asked them to down their tools for its own selfish interests.
"The union is being used by politicians to incite workers to take industrial action yet Kerugoya and other hospitals are now running smoothly. This is politics ... the workers should continue working," she said.
She spoke at the county headquarters in Kutus after assenting to the appropriations bill.
Ms Waiguru said Sh1.8 billion was factored into the supplementary budget for improving the health sector so there should be no cause for alarm.
"We now have enough money to buy medical equipment and drugs for hospitals. Those politicising the Sector should stop," she said.