Heavy rainfall over last weekend prompted long delays in train services.
Journeys from Stockholm to Malmö were extended by more than three hours after a Trafikverket (the Swedish Transport Administration) building was flooded in Norrköping.
Trains remain affected around Norrköping with some cancellations to services from the city to Linköping, according to a Transport Administration statement.
Speaker systems are out of service in Norrköping, Nyköping, Hälleforsnäs, Kimstad, Linghem, Vagnhärad, Läggestad, Vikingstad, Kolmården and Åtvidaberg, while electronic signs on platforms are back in service.
Further disruptions have been reported between Varberg and Borås and buses are plying the routes around Tanum in western Sweden after a derailment at the weekend.
Services have been completely closed since Saturday with rainfall flooding the tracks. The water was pumped away on Monday and trains are expected to resume running as normal on Tuesday.
"Trains will begin running at low speed, so we will notice if the embankment has been damaged," Anna Hansson at the agency told the Svenska Dagbladet daily.
Stockholm-Malmö services returned to normal already on Monday, but full service is not expected to be resumed until Friday, according to the agency.