Spokesman Tomas Hulan confirmed the discovery, saying that it was sent for testing at Prague's Institute of Criminology.
Police already had found 12 illegal weapons in a search following the explosion that killed Ambassador Jamal al-Jamal, a career diplomat who had only started his posting in October.
It remains unclear what caused the safe to explode but the ambassador's death is being investigated as a case of negligence while the found of the explosive and weapons are considered illegal arms possession.
Police said they received a letter from the Palestinian authorities saying the weapons were given to them as gifts by the officials of the former communist Czechoslovakia. Czechoslovakia was part of the Soviet bloc that had warm ties with the Palestinian Liberation Organisation.
According to police, the Palestinians said the weapons were never used and always kept in a safe.
Police said experts are trying to determine whether the weapons were used in any criminal activity in the past. The ballistic testing might take weeks, police said.