Mr Gusinsky's lawyer said he had not been told the nature of the charges, but the Interfax news agency reported that they were related to the alleged illegal transfer of assets abroad.
Mr Gusinsky - who is reportedly outside of Russia at the moment - has frequently clashed with Russia's President, Vladimir Putin, particularly over his Media-Most group's coverage of the war in Chechnya.
News of the charges came amid reports that Mr Gusinsky had settled a debt row with Russia's largest energy company, which had led to him facing embezzlement charges earlier this year.
The prosecutor's action followed Mr Gusinksy's failure to answer a Moscow court summons on Monday.
Interfax reported that Media-Most had issued a statement dismissing the charges and arrest warrant as "illegal actions" by the Russian prosecutor.
Chechen campaigns
Correspondents say the Kremlin under Mr Putin has come to regard the Media-Most group as a thorn in its flesh.
NTV and other outlets in Mr Gusinksy's media empire frequently criticised Russia's military campaigns against Chechen rebels.
Mr Gusinsky's lawyer, Genri Reznik, said the prosecutor's office had "refused to tell us of the contents" of the charges.
The lawyer would not say where Mr Gusinsky was, only that he was "in Europe", and that he had no intention of turning up at court or at the prosecutor's office.
"My client does not want to become a victim of arbitrary action, causing his family to suffer again," Mr Reznik said.
In June, he was accused of embezzlement over dealings with the giant energy company, Gazprom, and jailed for three days.
His imprisonment provoked an international outcry and led some Russian commentators to question Mr Putin's commitment to press freedom.
But reports say Gazprom has now settled its row over debts it says it was owed by Media-Most.
The two companies are due to submit their agreement for approval by the courts on Tuesday.