MOSCOW — A court ordered Russia’s largest privately owned business conglomerate on Wednesday to pay $2.3 billion to the country’s state oil company in a case closely watched by investors worried about the unraveling of private property rights.

The conglomerate, Sistema, called the ruling troubling because the penalty was imposed in part for transactions that preceded a planned initial public offering, suggesting that any company preparing to go public could be seen as violating the law.

“The judge has in effect cast into question the legality of standard corporate procedures such as preparations for an I.P.O., and buyback and cancellation of a company’s own shares,” said Sergei Kopytov, a spokesman for Sistema. “We think that this ruling will have a significant negative impact.” Sistema said it would appeal the ruling.

The dispute dates to the nationalization in 2014 of the Bashneft oil company, a former subsidiary of Sistema. The nationalization was another zigzag in Russia’s on-again, off-again embrace of private property in the post-Soviet period.