An agency affiliated with Bay Area's transportation commission voted Wednesday to buy a San Francisco building for $93 million as a new regional government headquarters, despite pleas from Oakland leaders not to leave their town.

The vote was 8-6 by the Bay Area Toll Authority, a sister agency of the Metropolitan Transportation Commission. All East Bay members of the toll authority opposed the purchase of the building at 390 Main St.

Several state lawmakers from the East Bay also oppose the move, saying it's wrong to proceed at least until a state audit is done to determine whether it's legal to use bridge toll money to buy the building.

Supporters of the purchase say it makes sense to locate the region's transportation, air pollution and shoreline regulatory agencies in a single building to tackle common problems such as reducing greenhouse gases.

"This purchase culminates years of effort to get land use, air quality, transportation and bay agencies under a single roof," said Randy Rentschler, a toll authority spokesman.

The Bay Area Air Quality Management District and the San Francisco Bay Conservation and Development Commission also plan to move into the building.

The Association of Bay Area Governments has voted not to join the move.

The building is owned by a group of investors, including Amerimar Enterprises, Angelo Gordon and Company, and Barnes RHPO Partners.

The investors bought the building for $60 million in 2010. Its value has increased since then because of demand in the South of Market area of San Francisco for commercial space to house digital, Internet, social media and biotech companies, according to a report by appraisers.

Contact Denis Cuff at 925-943-8267. Follow him at Twitter.com/deniscuff.