"Some of this work was not completed in time and we did not get all the tracks back at 5am this morning. We now have two of four tracks open," said Ola Nilsson at the Swedish Transport Administration (Trafikverket) to the TT news agency.
Stockholm public transport operator SL has advised that delays of up to an hour are likely on some routes, with the prospect of cancellations to be expected.
"This means long delays and the risk that many trains will have to be cancelled," Nilsson confirmed at around 8am on Monday.
The disruption affects both commuter and long-distance trains in both north and southbound directions.
Årstaberg station is not accessible at all and Älvsjö is not accesible for northbound traffic.
Årstaberg station remained inaccessible southbound at 1.30pm on Monday and SL advises that this is likely to remain the case until 5am on Tuesday. Northbound trains had however resumed stopping at the station.
SL have confirmed that long distance rail services are being given priority on the tracks, with replacement buses deployed on the route Huddinge-Älvsjö-Årstaberg-Liljeholmen route.
According to information on SL's website on Monday morning, it was hoped that full service will be re-established by 11am on Monday.
According to information published by SL at 1.30pm, with the exception of Årstaberg (detailed above), most lines had returned to normal service.
The delays affect all commuter train service heading into Stockolm's Central Station.
The City Line tunnel project is a massive infrastructure investment involving the drilling of a 6 kilometre rail tunnel under central Stockholm to provide increased track capacity through Stockholm.
The line is scheduled to enter service in 2017.