The 48 people injured Saturday when a moving train collided with a parked train at a station brought the 2009 total to 68 passengers.
"Any injuries on one of our vehicles is one too many," said Judson True, a spokesman for the rail agency. "As we've already demonstrated since this collision, we're willing to take all necessary steps to improve safety on the system."
He said the rail agency reports all injuries to the federal government.
The injury rate in San Francisco was almost identical to that of Boston and slightly higher over the last five years than rates for comparable light-rail systems in San Diego, Dallas, St. Louis and Portland, Ore.
Meanwhile, the National Transportation Safety Board on Wednesday confirmed previous reports that it was focusing on human error as the cause of the crash after finding no indication of mechanical or systems failure.
The operator of the San Francisco Municipal Railway train responsible for the collision told NTSB investigators he blacked out before the crash after shifting his train from automatic to manual control.
The accident occurred when a westbound train smashed into another train parked at West Portal Station, located in a quiet neighborhood filled with cafes and shops.
Four people were seriously injured, including the driver of the moving train. Only two people remained hospitalized Wednesday, both in good condition.
The NTSB said its inquiry found no problems with the train's brakes or any other mechanical issues that would have led to the accident. The inquiry also found no fault with the signaling system.
Investigators were still reviewing the health history of Henry Gray, the 61-year-old operator, who switched his train to manual control in a tunnel near the station about 24 seconds before the accident.
There was no indication Gray used the emergency brake before impact, or a device each train is equipped with known as a "dead man's lever," a grip that operators engage when switching from automatic to manual mode. When let go, the spring-loaded lever stops the train.
The city's light-rail trains are supposed to be equipped with surveillance cameras that could have captured Gray's blackout. But the San Francisco Municipal Transit Agency said the cameras were not installed on the train that crashed. The accident was captured by station surveillance cameras, but no footage captured the actions of Gray, officials said.
The NTSB also said there was no indication that mobile phone use played any role in the crash. Still, Gray's cell phone records were subpoenaed as part of standard procedures.
The San Francisco Municipal Transit Agency said Gray, of nearby Richmond, started as a San Francisco bus driver in 1979 and switched to light rail in 2007. Both his commercial and personal driver's licenses show a clean driving record, according to the California Department of Motor Vehicles.
The San Francisco rail agency released details Wednesday of immediate steps it was taking in an effort to make the system safer, including citing drivers who switch from automatic to manual mode without authorization.
Agency policy forbids the switch to manual outside of a station without consent from someone in the central control unit. But Irwin Lum, president of San Francisco's transit workers union, has said the agency has condoned the practice to keep trains running on time.
The last time a San Francisco Municipal Railway passenger died in a train accident was in 2000, according to the federal transit administration. The data did not include pedestrians injured or killed by light-rail trains.
San Francisco cable cars and light-rail trains have killed eight pedestrians since 2006, according to transit agency statistics.
State transit safety regulators said the agency has complied with all but one recommendation from a 2005 safety audit. The transit agency had not completed revisions of its rules and instructions handbook, said Terrie Prosper, spokeswoman for the California Public Utilities Commission.
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Associated Press Writer Jason Dearen contributed to this report.
