Czech police spokesman Tomas Hulan confirmed the discovery, adding the unidentified explosive had been sent for testing to the capital's Institute Of Criminology.
Police had already found 12 illegal weapons in a search following the blast on January 1, prompting the Czech Foreign Ministry to accuse the Palestinians of breaching international obligations.
The Palestinians said the weapons were not illegal and dated to the Cold War. At that time Prague had a close relationship with the Palestine Liberation Organisation, training its operatives and frequently hosting its leader, the late Yasser Arafat.
Ambassador Jamal al-Jamal died after the safe exploded. The career diplomat 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. Police ruled out an attack on the diplomat.