The problem is not expected to be resolved until 6am on Thursday, said the Swedish Transport Administration, which urged travellers to keep an eye on their departure for more information.
All trains on the route are affected by the delays and cancellations, including Arlanda Express to the airport, SJ's long-distance and inter-city trains between Uppsala and Stockholm, and SL's commuter trains between Märsta/Uppsala and Stockholm City.
The delays are due to a problem with the tracks between Upplands Väsby and Häggvik.
There were further headaches for commuters on Wednesday morning after a wheel loader hit a flyover between Häggvik and Norrviken at around 10.30am, bringing trains to a standstill south of Upplands Väsby.
The Local Sweden's editor Emma Löfgren was one of those passengers caught in the disruption.
Currently stuck on the train after a wheel loader had a wee accident between Norrviken and Häggvik, as if the train disruption we already knew about wasn’t enough. https://t.co/l4fQ9YFmTD
— Emma Löfgren (@ekjlofgren) November 6, 2019
After an inspection of the flyover, traffic resumed at around 11.30am, but delays caused by the separate track problem between Upplands Väsby and Häggvik were still expected to continue until Thursday morning.
track problem – (ett) spårfel
delay – (en) försening
cancelled departure – (en) inställd avgång
train – (ett) tåg
commuter train – (ett) pendeltåg
Do you want to learn more public transport vocabulary to help you survive your commute in Sweden? Here's The Local's guide.