Two 17th-century crowns originally belonging to King Karl IX and Queen Kristina were stolen along with a royal orb, officials said.
According to Swedish radio the offenders took two crowns and a royal orb known as a "riksapple" from the ancient cathedral in Strangnas, west of Stockholm, around lunchtime on Tuesday.
Britain's own crown jewels were almost stolen in 1671 by Anglo-Irish Colonel Thomas Blood, who was captured as he fled the Tower of London with St Edward's Crown, the Scepter with the Cross, and the Sovereign's Orb.
The thieves have not yet been captured. In the statement, police described the motorboat as a small open boat, although it was uncertain what colour the boat was. "Two men hurriedly jumped on board and it sped off".
The crown jewels of Charles IX and his wife Christina were buried with them upon their deaths in 1611 and 1625 respectively.
Police made public the details of the robbery in an attempt to identify the thieves. "We have some different information about how exactly the boat looked", Thomas explained.
"I knew immediately that they were burglars because of the way they were behaving". The stolen items were on display at an exhibition in the cathedral, and visitors were inside at the time.
Police sent out a helicopter and boat to hunt for the thieves but found nothing.
Maria Ellior of the Swedish police's National Operations Department told TT that the items are "impossible to sell".
Agnevik added: "But if they are pros, we may not get the items back or find whoever did this".
Christofer Lundgren, dean of the cathedral, said: 'This is part of the national cultural heritage - this is a theft from Swedish society'.