One of the men is believed to be a 35-year-old dentist from Small Heath. A third man survived and notified the authorities.
The man's family said they were notified of his death on Saturday at 19:00 BST.
The Foreign and Commonwealth Office said: "We can confirm the death of two British nationals in Malta."
Malta's police force said the two men were both 35-year-old British nationals.
They were swimming at the Blue Lagoon, in Comino, at about 15:30 when they got into difficulties.
"Members from the Armed Forces of Malta went... to assist the two persons," the force said.
"One person was taken by a private boat to Imgarr whilst the other person was airlifted to the Gozo General Hospital by a helicopter.
"Unfortunate they were both certified dead."
The force added police investigations were under way.
Two British men, including one from Birmingham, have been reported drowned on holiday in Malta.