Benami properties are those that are not bought and registered in the name of their real owner. Holding benami properties is an offence.
Mr Modi is also a key accused in the Rs 12,717 crore Punjab National Bank fraud case.
"The court has issued a bailable warrant against Modi," the official said.
He said the department was investigating the matter against Mr Modi since 2017 but declined to disclose the details of the property.
The official said the probe revealed that Mr Modi had given a false statement to department
"When we went to his residence in Worli recently with summons, we found it locked," the officer said. A case was later filed in the court.
The court adjourned the case till next month.