A man from Msida is expected to be arraigned shortly, charged with hunting-related offences.
The police said on Friday its Administrative Law Enforcement Section received a report on Thursday at 7.15pm that shots were heard in the Żebbiegħ area probably aimed at a protected black stork.
The police were also informed that a parked vehicle in the area possibly belonged to the shooter.
Later, officers from the Rapid Intervention Unit stopped the car that was being driven by a 32-year-old man in the Għargħur area.
A modified firearm that was loaded and hidden in a compartment behind the seat was found and the man was arrested.
In a search at his residence later, the police confiscated another firearm as well as other items.
The man is being held at the police headquarters for questioning.