Some 97 passengers were left sitting on the SJ X2000 train bound for Odense in Denmark on Sunday evening as technicians worked to solve the problem.
The train left Stockholm at 2.20pm with an arrival time in Malmö of 6.42pm. At around 7pm, tunnel technicians detected smoke in the tunnel.
The source of the smoke was traced to a power outage caused by an errant helium balloon complete with a long ribbon which had got itself entangled in some power lines.
Both tracks through the tunnel were out of service for 30 minutes, before technicians were able to get one track back into service. The other track however remained out of service throughout the evening causing long delays in traffic to and from Copenhagen.
On that track sat the train with 97 passengers on board.
"After they had sat there for around 80 minutes, we decided to evacuate them," said Thorvald Svahn at SJ to the local Sydsvenskan daily.
The problem was solved at around 10.30pm and all passengers were then able to continue their journey to Öresund.