OAKLAND — The same agency tasked with overseeing the ballooning costs of building the eastern span of the Bay Bridge also saw a doubling of the construction costs to renovate its new San Francisco office space, bringing the final price tag for the move to nearly $258 million.

The regional Metropolitan Transportation Commission will share the new office with the Association of Bay Area Governments. Both agencies are moving from the building they shared with BART at 101 Eighth St. in Oakland, and will officially move into their new south of Market digs on Monday. The Bay Area Air Quality District, a regional regulatory agency, is scheduled to join them later this month.

MTC’s decision in 2011 to purchase the former post office at 375 Beale St. in San Francisco was controversial from the start, sparking a state audit to determine whether it was legal to use bridge tolls to buy and renovate the property. Congressman Mark DeSaulnier (D-Concord), who initially requested the audit, later introduced SB613, which was signed into law in 2013 and prohibits the agency from using toll fares to purchase another office building.

The state audit concluded the agencies’ move was “likely legal,” but warned that toll payers could be left on the hook paying for the new building. Since the time of the audit, construction costs only increased.

MTC initially allocated $93.1 million in toll funds to purchase the building and $74 million to renovate it. The renovations have more than doubled to $159.7 million, bringing the final price tag to $257.8 million. Randy Rentschler, a spokesman for MTC, said the construction cost overruns were attributed to three main factors: The U.S. Drug Enforcement Administration, which occupied a floor of the building at the time of purchase, took 11 months longer than expected to relocate. The commission decided to carve out a new atrium to draw light into the center of the building. And, the cost to seismically retrofit the building, initially estimated at $1 million, turned out to be closer to $10 million, Rentschler said.

“When you turn an eight-story industrial space into offices, you don’t just paint the walls and show up,” Rentschler said. “Turning it into an office building, (the commission) just decided to do more.”

Oakland City Councilmember Rebecca Kaplan, who opposed the move, blasted the agency for underestimating construction and seismic retrofit costs and not accounting for anticipated delays from the DEA. Kaplan questioned whether the MTC was learning from a pattern of costs overruns and project mismanagement.

“The building is a microcosm of a bigger problem,” Kaplan said.

She said it was ironic that some of the money used to finance the new building — about $33 million, according to MTC records — came from money that was supposed to be allocated for the construction of the eastern span of the Bay Bridge, a $6.4 billion project that continues to need repairs. The latest glitch involves faulty sealing work that allowed salt water to corrode rods meant to keep the bridge safe during a major earthquake. A bridge committee last week approved a $15 million plan to fix the grouting work.

Disability rights advocates had also warned that the new site, which is roughly a half-mile from the nearest BART station, would make it more difficult for seniors and people with disabilities to attend meetings. MTC spokesman John Goodman said the agency will provide a shuttle between the Embarcadero station and the new office when the commission or its subcommittees are meeting. He said the shuttle costs roughly $75 per hour.

“We’re hopeful it will help people getting over there,” said Sheri Burns, the executive director of the Silicon Valley Independent Living Center, a disability rights advocacy group. “Seniors and people with disabilities want to be involved and should be involved whenever (the MTC is) … making decisions on what public transit projects will be funded.”

The 397,000 square-foot space is larger than the agencies needed, but Rentschler said most of the remaining space, 180,000 square feet, has already been leased. FasTrak, geotechnical engineering firm Rutherford+Chekene, telecommunications provider Twilio, and structural engineering firm Degenkolb all have contracts to move in, netting the agencies $6 million in revenue the first year and $8 million the following year, Rentschler said.

The San Francisco Bay Conservation and Development Commission, a state agency, is also expected to move in, which would bring the building to nearly full occupancy. Income from renting the building will be returned to the toll authority’s reserve fund, which the agency maintains in order to issue bonds, Rentschler said.

The move to San Francisco leaves the agencies’ Oakland offices vacant. Rentschler said the East Bay Asian Local Development Corporation put in a bid for the space, but BART, which already owns roughly a third of the building, opted to try to buy the entire building instead. BART spokesman Jim Allison said the transit agency is interested in moving its police headquarters there, and eventually, commercial offices.

Once the deal is negotiated, Allison said BART’s board of directors would need to approve the purchase.

The MTC took heat for leaving Oakland and leading the charge to move into the new digs, which some called speculative. Now that the transition is nearly complete, Rentschler said the renovated building is “somewhat aspiring and somewhat modest.”

“It’s certainly not extravagant,” Rentschler said. “It’s stripped down. … Everyone was very mindful in trying to find that balance.”

Erin Baldassari covers transportation. Contact her at 510-208-6428, or follow her on Twitter: @e_baldi.