Bauer’s Intelligent Transportation, a private bus company that transports tech workers to their jobs in Silicon Valley, will no longer be allowed to use Muni bus stops and participate in the city’s shuttle program, the Municipal Transportation Agency announced Thursday.

The decision is a blow for Bauer’s, which has faced criticism from the Teamsters Union and the Board of Supervisors because of its conflict with drivers over pay, benefits and unionization efforts. The supervisors passed a resolution last week urging the MTA to remove Bauer’s from the shuttle program.

Bauer’s said it would appeal the MTA’s decision revoking its permit.

In a letter to Bauer’s on Thursday, the MTA said its decision was based largely on factors unrelated to the labor dispute.

It criticized the company’s “repeated failure to comply” with traffic laws, noting that while Bauer’s service constitutes about 10 percent of commuter shuttle stops, 34 percent of complaints were related to Bauer’s vehicles. Half of those complaints pertained to Bauer’s buses driving on streets with weight restrictions. Another large number of complaints were about the buses stopping in unauthorized locations.

“Bauer’s continued violations of these requirements has contributed to unacceptable traffic congestion on weight-restricted streets and impeded safe and efficient Muni operations by blocking access to Muni stops,” wrote Tom Maguire, director of the MTA’s Sustainable Streets division. “These results are inconsistent with the goals and purpose of the commuter shuttle program.”

Gary Bauer, CEO of the bus company, attributed the high number of complaints to people assuming every shuttle bus was from Bauer’s. The company is getting “punished for doing a good job branding the company,” he said.

Bauer said the Teamsters were the real driver in the MTA’s decision to revoke his company’s permit. “It’s more about the union than anything else,” he said.

Indeed, the MTA referred to the union dispute in its letter revoking Bauer’s permit. It said the company had an insufficient “service disruption prevention plan” that would allow the buses to maintain consistent and efficient service. In other words, the company’s dispute with Teamsters was likely to result in more protests and pickets, in turn causing disruption to city buses.

“Granting a commuter shuttle permit to Bauer’s under these circumstances could lead to further disruptions in Muni service, blockage of bicycle and travel lanes, and safety hazards for San Francisco transit riders and road users,” Maguire wrote.

Emily Green is a San Francisco Chronicle staff writer. Email: egreen@sfchronicle.com Twitter: @emilytgreen