Some 5,000 Kenyan medical experts went on strike on Monday after negotiations with government over a pay rise collapsed.
Nairobi Police Commander Japheth Koome told AFP that police had launched an operation to return the patients to the hospital, as videos on social media showed them climbing over the hospital walls and running down a nearby highway in the capital.
"We have already arrested dozens of the... patients who had escaped in an ongoing operation," Koome said.
"The doctors messed (up) by leaving the patients unattended."
Some 5,000 Kenyan doctors, pharmacists, dentists and nurses went on strike on Monday after negotiations between unions and government over a pay rise collapsed on Sunday.
Unions are demanding a 300-percent pay rise for doctors and 25- to 40-percent pay rise for nurses that was agreed upon in a 2013 collective bargaining agreement, but has yet to be implemented.
Hundreds of striking workers marched to the National Treasury wearing lab coats, masks and theatre caps before police dispersed the crowd with tear gas.
"No amount of intimidation, no amount of propaganda will make us change our determination," said Kenya Medical Practitioners, Pharmacists and Dentists' Union (KMPPDU) chairman Samuel Oroko.
He said the public should be prepared for "the longest strike ever" as doctors would not return to work until their demands were met.
The striking doctors and their supporters point to recent scandals in corruption-plagued Kenya in which millions of dollars have been embezzled or gone unaccounted for, while the doctors struggle to get their wage increases.