The Kremlin earlier denied the searches were retribution for revelations about people close to President Vladimir Putin that were published by a newspaper controlled by Prokhorov.
The searches of the offices of Onexim, which manages Prokhorov's assets, were conducted together with the tax service as part of a criminal investigation related to Tavrichesky Bank in St. Petersburg, the Federal Security Service said on Friday.
A year ago, the central bank selected IFC bank (International Financial Club), in which Onexim has a stake, to rescue Tavrichesky Bank and granted a 10-year loan of 28 billion roubles ($422 million) to Tavrichesky for the procedure. Tavrichesky is supposed to merge with IFC Bank in 2022, the Central bank has said.
Onexim and IFC bank, which was one of the Onexim's businesses at which searches were conducted, were not available for immediate comment on Friday evening.
The Federal Security Service said it had obtained data on tax law violations at "a number of commercial structures" after the searches and handed over the documentation to specialists for further investigation.
The Service did not say whether these unnamed commercial structures were part of Onexim and did not say how the rescue programme could be related to tax violations. It is also not clear which criminal investigation the service means.
RBK newspaper, controlled by Prokhorov, has in the past few weeks published reports about the commercial interests of Putin's son-in-law, and about associates of Putin implicated in the "Panama Papers" leaks about offshore assets.
($1 = 66.2744 roubles)