The 31-year-old man was at the time of the accident helmsman on the boat.
On Friday, the Copenhagen District Court found that he must have drunk five beers just before the collision - when he was on duty.
Others in the crew must also have been under the influence of alcohol when they were arrested by the police.
In the morning, six hours after the accident, the 31-year-old must have had 0.457 per mille in his blood, writes Ekstrabladet.
The man has explained to the police that he did not see the Danish ship until the last minute and that he then tried to avoid a collision.
He was arrested on Thursday for aggravated drunken driving, aggravated negligence in maritime traffic and aggravated causing another person's death.
He is currently in Swedish custody awaiting extradition.
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The ship accident outside Ystad - in 60 seconds