"The commuter trains can't stop at the new stations, Stockholm City and Stockholm Odenplan; and the trains going south can't stop at Årstaberg," Christian Hoffmann, spokesman for Stockholm Public Transport, SL, told Radio Sweden.
"About 300,000 people use the trains every day," he added.
SL has re-opened older tracks and platforms to alleviate the problem, but severe delays are expected.
"The problem will last this evening...we don't know about tomorrow yet," Hoffmann said.
He urged passengers to check the SL website at www.sl.se for updates.
The six-kilometre (four-mile) Citybanan opened in July this year.