The discovery was made by labourers close to the royal palace and in front of Stockholm's Grand Hotel during renovation works to a quay.
"The discovery of the wreck is extremely interesting given the place where it was made. There was a naval shipyard on this spot until the start of the 17th century," Maritime Museum director Hans-Lennarth Ohlsson said in a statement.
A couple of weeks ago, an excavator found something unusual in his bucket. Marine archaeologist Jim Hansson at the Maritime Museum was called to Strömkajen below the Grand Hotel, where he quickly realised the value of the sensational find.
"We were super-excited. It may sound a little strange when one finds little excavated pieces of parts of a ship, but I have never seen anything like it," he said.
With the exception of another ship found in 1896, all other shipwrecks uncovered in and around the Stockholm harbour have featured planks that were nailed together.
"We really know nothing about this technique other than that it was used in the east," added Hansson.
Hansson guesses that the ship is from east of the Baltics, possibly from Russia. The ship's position, well into the quay, reveals that it is from the 1600s or earlier. The wreck was not necessarily linked to the yard, however, and archaeologists have been unable to say how long before 1700 it might have sunk.
Marine archaeologists will send samples to Denmark's Copenhagen National Museum for analysis to be dated as precisely as possible, with results expected by January 2011. In addition, they will monitor the rest of the excavation.
"It is pretty damn nervewracking. It is rare that an archaeologist gets to take a part in something like this. One gets to leave the kids at home and stand in a pit of mud at Christmas," Hansson joked.
In 1961, the Vasa, a Swedish warship, was salvaged from just outside Stockholm harbour. The ship, which foundered on her maiden voyage in 1628, was largely intact and has since become one of Sweden's most popular tourist attractions.