Basmanny court ruled earlier Friday to freeze shares in the state pipeline monopoly after the Prosecutor General's Office launched a probe into illegal privatization of shares and abuse of office.
A court source said the shares had been illegally distributed among various companies and were later discovered at Registrator ROST, one of Russia's largest companies that services share registers.
Ilya Zafakayev, head of Registrator ROST's PR service, said the company suspended transactions in Transneft preferred shares.
But Transneft vice President Sergei Grigoryev said the suspension of trading would not affect its activity, as the shares are preferred and not voting shares.
"These shares are held by individuals and are not voting [shares], and the company's management has nothing to do with them," he said, adding that the state held 100% of voting shares.