The 18-month program will allow the buses to stop at about 200 of the city's 2,500-plus Muni bus stops if they pay a fee, Mayor Ed Lee said.
The fee for the bus operators, which transport from local stops such as the Alameda County Fairgrounds in Pleasanton, will depend on how many stops a bus makes daily. From Pleasanton, these buses serve employees for companies such as Google, Apple and Facebook as well as universities and hospitals.
Lee said the commuter buses provide an important service, providing more than 35,000 boardings per day in San Francisco.
However, he said the buses have also drawn political criticism from tenant advocates that have targeted them in protests over rising costs to live in the city. There have also been complaints that they cause Muni delays.
"I think the shuttles are here to stay, but they've got to get better coordinated," Lee said.
Board of Supervisors president David Chiu said the buses previously had no regulation by the city and were causing headaches in various neighborhoods around San Francisco.
"It was the wild, wild West out on our streets," Chiu said.
Muni director of transportation Ed Reiskin said the proposed program is expected to cost $1.5 million over the 18 months and will bring in that same amount.
California's Proposition 218 disallows a fee structure for the program that goes beyond the cost to provide the service, Reiskin said.
The 200 Muni bus stops will only be available to permitted operators, which will have to heed guidelines such as yielding to Muni, pulling to the front of the bus stop and avoiding steep streets, Reiskin said.
The rest of Muni's bus stops will be off-limits to the commuter buses, which will have unique placards to allow for better enforcement by the city, he said.
Reiskin said the agency's board of directors still needs to approve the program and will consider it at an upcoming meeting on Jan. 21.
The Bay Area Council, a business advocacy group, helped bring the various companies to the table to work with the city on the program, he said.
Veronica Bell, Google's manager of public policy and government affairs, said the company is "very excited to be working with the city."
Bell said, "We see this pilot program as a good first step."