Police probe Tom Tomsk over Pogrebnyak
Tom general director Yuri Stepanov told the club's website: "Following a newspaper report, [police] have opened a criminal case [against the club].
"The club continues to function normally. We will update our fans about the results of the investigation," he added.
The newspaper Novaya Gazeta reported last month that a third party had been paid $400,000 to obtain Pogrebnyak's transfer from Spartak Moscow to Tom in 2006.
Russia striker Pogrebnyak, who moved to Zenit St Petersburg in 2007 before joining Bundesliga club VfB Stuttgart two years later, and his agent, Oleg Artemov, have denied any wrongdoing.
Tom Tomsk have had financial problems in the past.
The club was saved from going out of business because of mounting debt in 2009 following the intervention of Prime Minister Vladimir Putin, who ordered seven of Russia's largest oil and energy companies to rescue them.