The conglomerate, which has assets ranging from farms to a cellphone operator, had hoped that by staying out of the political spotlight it could avoid legal entanglements. Executives seen as disloyal to the Kremlin have long been seen as targets, facing harassment and legal action. The onetime owner of the Yukos oil company, Mikhail B. Khodorkovsky, for example, was arrested after financing opposition politicians. While Mr. Yevtushenkov was placed under house arrest during Bashneft’s nationalization in 2014, because he had never dabbled in opposition politics, it was widely seen as a consequence of this business dispute.
“This conflict is causing a lot of harm to the investment attractiveness of Russia,” Aleksander Y. Abramov, a professor at the Russian Academy of National Economy and Public Administration, said in a telephone interview. “This case can create a precedent when any activity in the past can be contested, and property rights put in question, for any company.”
The dispute traces its origins to Sistema’s loss of its Bashneft oil subsidiary in the 2014 nationalization. Sistema had accumulated shares in Bashneft from regional elites, who had in turn acquired it years before from a regional government.
At the time of the nationalization, officials asserted that Russia’s federal government had erred in the original transfer of Bashneft to the regional government in 1993, and voided all subsequent transactions. The state property agency then sold a controlling stake in Bashneft to Rosneft.
The state energy company is now suing Sistema for mismanaging Bashneft, and stripping it of assets, demanding $3 billion in compensation. Sistema denies the allegations.
On Monday, Sistema declared a technical default on 3.9 billion rubles, or about $66 million, in loans. The company said the technical default, a formal notice triggered by its failure to comply with some conditions on part of its debt, had occurred because a court overseeing the case had frozen Sistema assets used as collateral for the loans.
The privately owned company said that it would repay the loans, and that it did not anticipate banks demanding early repayment.
“The situation is a direct consequence of the plaintiffs, who must have known that freezing our assets would lead to a technical default,” Mikhail Shamolin, Sistema’s director, said in a statement on Monday.
Rosneft did not respond to a written set of questions, but the company has previously defended the case as legally solid, and said the specifics should be debated in court, not the media.
The conflict has rattled investors, with Sistema shares falling about 3 percent on Monday.
The company had been trying to attract international investment into the Russian economy. This year, it carried out an initial public offering for one of its subsidiaries, Detsky Mir, which operates a collection of toy stores. The I.P.O. was the first in Russia since crisis.
It has also cast a light on the struggles facing Rosneft, which cannot raise money directly from international banks because it was sanctioned after the conflict in Ukraine. The sanctions ban any long-term lending to the energy company.
In an interview last month with RBC, a Russian business newspaper, Mr. Shamolin said the case could be easier to understand, if only there was a political context.
Sistema might defend itself, he said, “if there was some sort of logic, that was discussed in the press, that the company had behaved improperly — by the unwritten rules.”