Armed personnel opened fire on two passing vehicles they deemed suspicious outside the base in the city of Khomein, the semi-official ISNA reported, killing three people the report described as "martyrs".
A fourth person died from injuries sustained in the shooting later on Friday, according to the local governor.
The city’s public and revolutionary prosecutor said those involved in the shooting are under arrest, and that a judicial case has been opened for them. The wording of the state media report suggests the victims were civilians killed in error.
Tehran is reeling from intelligence lapses in the 12-day war which allowed its arch-foe to assassinate top military figures and wreak havoc on bases and nuclear sites.
Hundreds of civilians were killed in the shock campaign last month.
The shooting comes amid heightened domestic surveillance and arrests following the outbreak of war between Israel and Iran last month
Iranian authorities have detained at least 700 people on suspicion of collaborating with Israel, with hundreds reportedly arrested in Tehran as checkpoints have been deployed across major cities, and a new public hotline solicits tips for “suspicious behavior.”