The property, spread in 17 acres, was provisionally attached by the agency last year in September under the provisions of the Prevention of Money Laundering Act (PMLA).
The Enforcement Directorate had served eviction orders to the occupants in April this year after the owners failed to get any relief from appellate bodies.
"This property belongs to Ms Mandwa Farms Private Limited which was being controlled by Mallya," the agency said in a statement.
An ED team, from its zonal office in Mumbai, today pasted the possession orders on the farmhouse, which has an adjoining beach.
While the registered value of the property is Rs 25 crore, the ED said, its market value is over Rs 100 crore.
It said Ms Mandwa Farms Private Limited had appealed against the ED provisional attachment order before the Appellate Tribunal for PMLA which "dismissed" the application two days back.
"Accordingly, peaceful possession of the subject property (having present market value in excess of Rs 100 crore) has been taken by the ED today," it said.
The ED is probing Mr Mallya and others under criminal charges of money laundering in the alleged Rs 900 crore IDBI bank default case.