The San Francisco Municipal Transportation Agency (SFMTA) received a low score in an audit of its performance in delivering construction projects. Millions are reportedly wasted annually in delays and management inefficiencies.

“Some of these findings are very disturbing,” said Supervisor David Campos after hearing the report at today’s San Francisco County Transportation Authority (SFCTA) Board meeting. “We have heard repeatedly how there are limited resources that the MTA has available, but this audit points out… that a big part of the problem is that we’re not doing enough with the resources we do have.”

As the SFMTA seeks new revenue sources to fill budget gaps for the coming fiscal years, it is considering unpopular fee increases like a hike in Muni fares, which was quickly taken off the table by the SFMTA Board of Directors yesterday.

The SFCTA Board, which approves much of the funding for the SFMTA’s capital projects, requested the audit from CGR Management Consultants.

The numbers reported were sobering. In the third quarter of 2010, 29 projects with a total baseline budget of $800 million had gone over-budget by an estimated $90 million, excluding the Central Subway, and averaged 592 days in delay.

The consultants estimated that 5 to 10 percent, or up to $15,000,000, of the SFMTA’s capital budget could be saved with better project execution. Among the causes for waste, they listed weak oversight of capital projects, inadequate staff reports to the SFMTA Board of Directors, and the board’s own leniency towards granting extra time and money to projects.

“What we found, in reporting to the SFMTA Board, and their own monitoring, is that they compare themselves to the approved budget, not the baseline budget,” said CGR Principal Jim Ayers. “They ought to be using [the baseline] as a benchmark for showing how well or not well they’re doing.”

The SFMTA officially “concurred” with 17 of the recommendations provided by the consulting firm and “partially concurred” with two. One of the recommendations that met with “partial” agreement concerned a reorganization of staff which SFMTA Director of Transportation Ed Reiskin said would hurt the agency’s flexibility. The other suggested using public affairs specialists to hold community outreach meetings rather than SFMTA staff, who are paid a higher premium.

“I believe it’s important that [the project managers] make the time available to spend engaging, to go to community meetings to understand what the concerns are, because ultimately, that person is going to be held accountable,” said Reiskin.

Reiskin also rebuffed some of the numbers in the report, arguing that some items categorized as “overruns” were actually project expansions, as in the case of the ongoing Duboce and Church rail replacement and streetscape project.

Still, the new transportation chief welcomed the audit as a guide for reform.

“It’s a great thing,” said Reiskin. “I’d be lying if I said we in departments love when folks come in and audit us, but often the results can be very helpful.”