The Marco Polo passenger ferry, operated by TT-Line, ran aground near the southern city of Karlshamn early Sunday, with the vessel's 75 passengers safely evacuated.
Two crew members were issued fines for "recklessness in maritime traffic".
"They have not, despite limited vision, used all available and useful tools to determine the ship's position and to avoid the risk of collision," public prosecutor Adrien Combier-Hogg told AFP.
He noted earlier reports that the position system aboard the ship had malfunctioned, and said that since the ship was travelling in fog, the crew should have activated other systems -- such as radar -- to verify the position.
"They relied on the electronic navigational chart, despite the warnings and impaired vision," Combier-Hogg said.
For certain crimes, Swedish prosecutors can issue fines directly without taking the accused to trial.
One of the crew members was fined 40,000 kronor ($3,600) and the other 16,500 kronor.
On Thursday, local authorities said the cleanup operations could last up to a year.
Earlier this week, the coast guard said a streak of spilled oil stretched over five kilometres (three miles) out at sea.
By Thursday, however, aircraft could no longer detect oil on the surface, as it had sunk and begun to reach the shores.
On Friday, the coast guard said that the ship was still stuck, and that it had called in additional help from Sweden's Home Guard to assist in the cleanup.
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