The Norwegian merchant ship is believed to have collided with a recreational boat with four people on board, two adults and two young children, late on Tuesday evening.
A woman and a child have been found dead after the pleasure boat with the four people on board is believed to have collided with a 90-metre merchant ship late Tuesday evening.
A man and the other child were found alive shortly after the alarm was received around 10pm on Tuesday.
"I have arrested the captain partly on the grounds of flight risk because he is a resident of a country outside the Nordic countries and the EU, and partly on the grounds of risk of undue influence on a criminal investigation, for example on witnesses," said prosecutor James von Reis, in a press release.
The captain is also suspected of negligence in maritime traffic. The decision to arrest was made at 6:30 p.m. on Thursday evening.
The Swedish Maritime Accident Investigation Board has been granted access to the black box from the cargo ship. The box could be important in the investigation, Swedish newspaper Aftonbladet has reported.
The Swedish Maritime Accident Investigation Board has launched an investigation in which the cargo ship's so-called black box could play an important role.
"We have downloaded it with the assistance of the police, but we have not had time to look at it. We will not do so until next week," Björn Ramstedt, who is investigating the accident for the Maritime Accident Investigation Board, told Aftonbladet.
"It is hoped that it will contribute to a fairly large part of the investigation. There may be audio recordings of what is said on the bridge when the ship is being driven."
According to Ramstedt, the investigation also needs to review the ship's navigation bridge, radar settings and electronic charts.
The investigation will also examine the motorboat and review the subsequent rescue operation.