Viktor Sviridov, former head of the prison service's transportation department, had been accused of extorting 10 million roubles ($160,000) from the service's deputy head, Alexander Sapozhnikov, according to local media reports.
The case had drawn little media attention until Sviridov shot himself shortly after the verdict was handed down at Moscow's Chertanovo District court on Wednesday afternoon.
Uliana Solopova, a spokeswoman for the Moscow City Court, confirmed the incident and said the court was trying to work out how Sviridov had managed to obtain a weapon. Russian courts generally have metal detectors and security guards at the entrance.
Alexander Kotelnitsky, a lawyer for Sviridov, told Russian news agencies that his client had been suffering from late-stage cancer.