A spokesman for the prosecutor-general's office said an order to seize the property had been issued but gave no details.
Gusinsky is now under house arrest in Spain pending a decision on Russia's extradition request on fraud charges, which he denies.
Most Russian liberals and Western politicians have denounced the proceedings against Gusinsky and his nationwide Media-Most empire as an attack on freeom of the press.
Interfax quoted prosecutors as saying the move was to back creditors' claims and ensure the possible confiscation of the property if the fraud case succeeds.
The seizure of Gusinsky's villa followed a lawsuit filed earlier this week by a branch of Media-Most's key creditor, gas giant Gazprom to take over 19 percent of the shares of NTV television, Gusinsky's most valuable asset.
Gazprom-Media, which already has 46 percent of NTV, Russia's only independent nationwide television station, undertook the action a day after the apparent collapse of talks in the Kremlin aimed at enabling CNN founder Ted Turner to buy a stake in NTV.
The Wall Street Journal, quoting sources close to the talks, has said Kremlin officials refused to provide guarantees that there would be no interference in the channel's operations. The Kremlin declined all comment on the report.
CLOSELY WATCHED BATTLE
The battle to secure control over NTV, which has been critical of President Vladimir Putin and his administration, is seen by liberals and many journalists as critical for the survival of the post-Soviet free press.
The director-general of United Nations cultural body, UNESCO, expressed his concern on Tuesday and urged Putin to uphold press freedoms. Putin last week repeated his belief that a free press was thriving in Russia.
The disputed 19 percent of NTV shares had already been turned over to the gas giant as part of a deal to eliminate Media-Most's large debts to Gazprom.
They were being held as collateral pending efforts to find a Western investor for NTV, but talks between Gazprom and Media-Most on the matter were broken off this month.
Turner was known to be interested in acquiring a stake of up to 25 percent in NTV. Media-Most currently holds 49.5 percent.
As part of their probe into dealings between Media-Most and Gazprom, prosecutors on Tuesday detained Media-Most finance chief Anton Titov on suspicion of conspiracy to embezzle.
Gusinsky, who built his empire during Russia's helter-skelter dash towards market reforms in the 1990s, says the fraud charges he is fighting are politically motivated.
The former theatre director has had a string of run-ins with legal authorities ever since Putin was sworn in last May.
Within days, armed tax office police raided Media-Most's headquarters and the following month Gusinsky spent three days in jail on fraud charges that were later dropped.
The media magnate says a government minister promised him freedom if he agreed to sell his empire to state-linked gas behemoth Gazprom. Gusinsky later reneged on the deal, which he said had been signed under duress.
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