Under Russian law, a probe can be launched against an employer over wage delays of over two months.
"It has been established that the company's debt in wages to its employees for July and August exceeds 60 million rubles [$2.3 million]," prosecutors said.
A report has been submitted to investigators, who are to consider launching a probe.
"We are not commenting on this information," an AiRUnion spokesperson said.
AiRUnion, in which the government holds an estimated 45% interest, suffered a cash crisis in late August amid rising aviation fuel prices. Flight delays affected hundreds of passengers who were left stranded in airports across Russia. The company's debt totaled around $800 million including fuel bills and back tax claims.
The government's move to provide fuel to support the alliance of airlines failed to rectify the situation, and the state-run Russian Technology Corporation, the Moscow government and the administration of Eastern Siberia's Krasnoyarsk Territory agreed to change the shareholders' structure and form a new national carrier on the basis of the AiRUnion alliance.
The Russian Technology Corporation, which will have a controlling stake in the new airline, said the reform process will take at least several months. The new airline will unite Atlant-Soyuz, Rossiya Russian Airlines, Kavminvodyavia, Vladivostok Avia and Orenburg and Saratov airlines.