In a statement today, the ministry says the Palestinians have promised to take measures to prevent such incidents in the future.
Police found 12 unregistered weapons in a search following the explosion. The Czechs said the arms were in breach of international obligations.
Ambassador Jamal al-Jamal died January 1 after an embassy safe exploded. The career diplomat had only started his posting in October.
The Palestinians previously said the weapons were not illegal and dated to the Cold War.