Two maintenance workers were struck and killed by a Bay Area Rapid Transit commuter train Saturday, two days into a labor strike that officials warned could cripple the area's transportation system starting Monday.

The workers were investigating a report of a dip in the track when a train on a routine maintenance run hit them, BART officials said.

One of the deceased was a BART employee and the other was a contractor. They were not immediately identified. One was acting as a lookout while the other inspected the track, officials said.

The train was running in automatic mode with an "experienced operator" at the computer controls, officials said in a prepared statement. Both of the workers who were killed had "extensive experience" with both freight and passenger trains, the statement added.

"This is a tragic day in BART's history," Grace Crunican, general manager of the public transit system, said in a prepared statement. "The entire BART family is grieving."

Spokesman Ben Fairow said the Bay Area Rapid Transit Police are conducting a full investigation, including interviews with everyone involved and drug testing of the train operator. The accident occurred at 2 p.m. between the suburban Walnut Creek and Pleasant Hill stations, officials said.

Transit employees went on strike Friday after a week of marathon negotiations broke down over work rules, including length of the workday and when overtime pay should kick in. BART, the nation's fifth-largest transit system, carries about 400,000 round-trip passengers each workday.

BART officials would not say who was operating the controls at the time of the accident, but some trains were being moved by managers, according to an Associated Press report. The two unions representing BART workers had warned of safety risks if managers were allowed to operate the trains during the work stoppage.

"The managers may very well have been train operators at one time, but still it's a bit of a struggle to come up to speed on short notice," Des Patten, a spokesman for Service Employees International Union Local 1021, said in a phone interview.

SEIU Local 1021 and Amalgamated Transit Union Local 1555 put out a joint statement expressing their "deepest sympathies for the families of the individuals who died in this tragic accident."

ATU officials said their 900 workers would not be picketing Sunday out of respect for the victims and their families.

An official with AFSCME Local 3993 confirmed that one of the workers who died was a member of its union who crossed the picket line. The American Federation of State, County and Municipal Employees was not on strike but had urged its members to support the other two unions, said Patricia Schuchardt, president of Local 3993.

Schuchardt said the unions had raised the safety issues during the negotiations.

"It's a very unsafe situation the agency gambled with," Schuchardt said. "Had there not been a strike, there would have been a lot more safety precautions out there."

The strike, the second by BART workers in four months, produced traffic jams and frustration Friday, but officials predicted the worst was yet to come.

Transportation officials said they believed many workers telecommuted or took the day off but would be back to their desks Monday. A BART spokeswoman said the system was considering adding more charter buses, but they would accommodate only a fraction of the displaced riders.

louis.sahagun@latimes.com

Times staff writers Jean Merl and Gale Holland contributed to this report.