About a dozen riot police in pickup trucks were out to monitor the protest, which was not authorised by the authorities.
Members of the 7,000-strong Kenya Medical Practitioners, Pharmacists and Dentists Union (KMPDU) have been on strike since March 13 to demand better pay and working conditions, disrupting health care at the country's 57 public hospitals.
Wearing white lab coats and blowing horns and whistles, the doctors chanted "solidarity forever" as they marched to the health ministry, where they blocked the entrance gates.
"We are more than willing to go back to the hospitals, but the effort being put by the government is not enough to end the human suffering," KMPDU deputy secretary general Dennis Miskellah said.
The union last week rejected an offer by the government that included paying arrears under a 2017 collective bargaining agreement, and hiring trainee doctors on permanent contracts.
In March, a labor court had ordered the union to suspend the strike and last week it set a 14-day deadline for the completion of negotiations to end the stalemate.
Kenyan President William Ruto, who has embarked on a program of cost-cutting measures since taking office in 2022, on Sunday ruled out any further concessions.
"We cannot continue to spend the money we do not have," he said.
"I am telling our friends the doctors that... we value the service they give to our nation, but we must live within our means."
Poor salaries and working conditions have led to an exodus of Kenyan medics to other African countries and further afield.
In 2017, Kenyan doctors staged a crippling 100-day nationwide strike that left public hospitals shut and patients unable to access basic medical care.
Dozens of patients died from a lack of treatment during the walkout, which ended after a collective bargaining agreement was reached.
But doctors have accused the government of reneging on some parts of the deal, leading to the current strike.