The NTV journalists resigned at the weekend after being ousted from their offices by a new management team installed by the state-controlled company, Gazprom, as a result of a disputed takeover.
The journalists say Gazprom was acting on behalf of the Kremlin, to bring a television station often critical of the authorities under political control.
The new charges, laid against the chief accountant of the TNT channel, Yelena Metlikina, have sparked fears that prosecutors may now be targeting the rebel journalists' new home.
Tax omission
Like NTV before its takeover on 3 April, TNT also belongs to the media magnate Vladimir Gusinsky, who is currently fighting extradition from Spain to Russia on corruption charges.
Journalists who refused to work for NTV's new managers have been broadcasting a scaled-down schedule of programmes from TNT, which reaches fewer viewers than NTV.
Ms Metlikina's lawyer, Pavel Astakhov, said investigators were planning to bring similar charges against TNT's director-general, Pavel Korchagin.
He said the case had originally been opened against TNT in September, and that the decision to pursue it now was connected with the dispute over NTV.
He said TNT had rectified a failure to pay 191,000 roubles in property tax immediately after tax police pointed out the omission.
Merger plans
Ten days ago Mr Gusinsky held talks in Spain with his former rival and fellow Russian exile, Boris Berezovsky, on a merger between TNT and Mr Berezovsky's TV6 station.
Broadcasts by the NTV rebels on Sunday confirmed that these negotiations were still under way.
The number of rebel journalists is disputed. The rebels themselves say they number more than 300, but NTV's new US-born director, Boris Jordan, says only 46 journalists have resigned.
Other managers said staff at the station's foreign bureaux were still deciding whether to leave or not.
The managers deny that they want to change editorial policies, but merely to improve the station's troubled finances.
NTV's former general director, Yevgeny Kiselyov, says he has accepted an offer to become acting head of TV6.
Reports in the Russian media have suggested that one of NTV's best-known news presenters, Tatiana Mitkova, could take his old job at NTV.