Two foreigners diving near Dwejra found themselves in difficulty due to the rough seas. While one of them managed to make it to shore, the other is missing, the Armed Forces of Malta said.
The missing diver is Greek.
The two divers had entered the water from the inland sea to swim through the narrow tunnel to reach the open waters.
The army said they received a message at about 5.15 p.m. informing them of the mishap. A search and rescue mission was mounted and a helicopter and a launch were deployed.
Attempts to search the area by divers was put off because of the rough seas.
"The northwesterly winds that gush through the tunnel put at great risk anyone who attempts to go through," an AFM spokesman said.
Peter Cordina, director of the Civil Protection Department, said his personnel at the heliport in Xewkija were alerted about the incident and were soon on the spot. They in turn raised the alarm with the AFM.
The search for the missing diver is expected to continue today.