High-speed rail services between the cities were redirected via Trollhättan and many passengers were obliged to take coaches from Herrljunga and Gothenburg.
Trains which connect with the main western line from Borås, Mariestad, Falköping and Nässjö are also at risk of delays.
Services are expected to return to normal by noon, according to the Swedish Transport Administration (Trafikverket).
"It's difficult to get hold of buses. Quite a few are needed to replace a train so they are chasing that up now," said Katarina Wolffram on the administration press office.
"A freight train is running past there now and it is going very slowly. Freight trains have priority and there are a few going past now," she said.
Meanwhile disruptions are set to continue to rail services from Stockholm north to Uppsala, Gävle, Borlänge, Falun, Sundsvall over the upcoming holiday weekend, according to the Transport Administration. The disruption is due to a downed power line and a fire south of Knivsta last week. The fire damaged essential equipment such as control signals and switches.
From 5am June 8th until 5am June 10th, no trains will run from Märsta - Knivsta and Arlanda - Knivsta because of repair work. A preliminary forecast is that rail services can be resumed on the morning of June 10th.
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In southern Sweden, meanwhile, the train strike has continued into its fourth day. A union spokesman told The Local on Wednesday that the strike shows no sign of ending soon.