The site is in a corner of northern Poland that was part of Germany until 1945 and the authorities suspect the remains are of ethnic German civilians, at least some of whom were probably killed by advancing Soviet forces.
"We are dealing with a mass grave of civilians, probably of German origin. The presence of children [...] suggests they were civilians," Zbigniew Sawicki, a Polish archaeologist supervising the exhumation, told Reuters on Wednesday.
"It is very puzzling that no personal belongings have been found among the remains [...] We have few clues as to how these people died, though there is a high probability they were war victims," Sawicki added.
Some 30 bodies were found with gunshot wounds, though the probable cause of death for many was hunger and cold, he said.
The first few skeletons were unearthed last October by construction workers who were laying the foundations of a new hotel in the town of Malbork, whose imposing castle - built by Teutonic Knights in the 13th century - is a major draw for tourists.
Harsh winter weather has now slowed the exhumation process.
In 1945, Malbork was the scene of heavy fighting between retreating German forces and the advancing Russians.
Adolf Hitler's army withdrew from Malbork, then known by its German name of Marienburg, in early March 1945 and the Soviet Red Army entered the town on March 17. German civilians had already been ordered to leave.
The region became part of a reconstituted, communist-ruled Poland after World War Two within borders which moved sharply westwards at Germany's expense, compensating Poland for the loss of eastern territories to Soviet Russia.
When the grave was discovered, authorities initially found the remains of just 60 people but the figure mounted rapidly.
"These people were buried in an appalling and inhuman manner," said Piotr Szwedowski, a Malbork city official.
"It was a serious shock to us... We are trying to exhume the remains in the most humane way possible and to ensure them a respectable burial," he added.
State prosecutors said Poland's Institute of National Remembrance would conduct research into the findings.
"We are looking for witnesses, or sources of information. We hope to find some leads because we still know virtually nothing about the mass grave and the victims," said Piotr Wojciechowski of the district public prosecutor's office in Malbork.