Only about 200 of Muni's roughly 600 vehicles are in service this morning, agency spokesman Paul Rose said.
Cable car service has been shut down this morning and major delays are occurring across the Muni system after a large number of workers called in sick today.
Commuters are advised to seek alternate modes of transportation. BART is honoring Muni fares all day today between Daly City and downtown San Francisco, Muni officials said.
The employee union, Transport Workers Union Local 250-A, was not immediately commenting on the sickout but has been in a contentious contract dispute with the San Francisco Municipal Transportation Agency.
The union voted last week on a proposed agreement with the SFMTA. The outcome of the vote was not immediately being released, but TWU Local 250-A president Eric Williams said on the union's website that it was an "unfair contract" and that the "city devalued our service as they proposed unreasonable take aways."
About 2,200 operators work for the agency. They are not allowed to go on strike but can call in sick.
San Francisco transit officials said the contract would increase operator pay to $32 an hour, making the operators the second highest paid transit workers in the country.
Union President Eric Williams called the proposal unfair and said in a statement on the union's website that the city had proposed "unreasonable takeaways in wages and benefits."
Calls and emails to union officials on Monday morning were not immediately returned.