By contrast, on-time performance for Regional Rail trains in December averaged 90 percent.
On Wednesday, 46 of 197 engineers were absent, and 80 of 389 conductors were out, SEPTA officials said.
Of 2,784 bus drivers and trolley operators, 198 were absent and 31 were late Wednesday.
"We expect everyone to come in for their assignments, and generally we get very high compliance," said Ron Hopkins, SEPTA's assistant general manager for operations.
"In cold weather, people truly do have emergencies at home . . . or they have difficulty in getting to their assignment points," Hopkins said, noting that many of SEPTA's passengers had similar difficulties Wednesday.
He said many engineers and conductors live far from the sites where they are supposed to begin their workday.
Late and canceled trains left many riders fuming at stations.
"There were thousands of people depending on them to show up and do their job so they could get to their own jobs," said Matthew Mitchell, president of the Delaware Valley Association of Rail Passengers. "My morning train was one of the ones that was canceled."
"I was stranded at 30th Street Station for almost two hours, trying to get a train on the Warminster line," said Bob Clearfield, the former chair of SEPTA's citizen advisory committee. "We kept asking crews that were coming in, 'Where's the train,' and they were saying, 'We have no crews.'"
SEPTA crews, whose members are permitted to call out absent until two hours before their shift begins, are not paid if they don't come in to work, Hopkins said. A single absence does not prompt disciplinary action, he said.
Operators are assessed points for calling out or being late or failing to show up for work, and a large number of accumulated points can lead to suspensions, he said, although that is rare.
Engineers, who often are scheduled to work six days a week, have been working without a new contract since 2009.
Willie Brown, president of Transport Workers Union Local 234, which represents bus drivers and trolley operators, said many employees could not get to work because of the weather.
"Not everybody can get around. . . . When the public is stranded, so are we," Brown said. And he said some operators were ill Wednesday after SEPTA sent them into the cold streets Tuesday to relieve drivers of buses that showed up hours late, or not at all.
Brown said many bus drivers and trolley operators live in New Jersey or Delaware, far from their duty posts in Philadelphia, and many were unable to get to work in the city.
"Bus drivers are people, too," Brown said.
Representatives of the Brotherhood of Locomotive Engineers and Trainmen, the union that represents SEPTA engineers, and the United Transportation Union, which represents conductors, could not be reached Thursday afternoon.