The breaches included insufficient pre-flight safety controls, a failure to inspect all cargo at Sheremetyevo airport and faulty baggage checks of passengers, Russian news agencies reported, quoting an official.
"Multiple violations of labour law have been found at Aeroflot, including some that negatively impact on flight safety," Marina Gridneva, a spokesperson for the Russian prosecutor general's office was quoted as saying.
Gridneva said flight crews were not being given enough time to rest and pointed out "flagrant breaches of the law" had also been found at Sheremetyevo, an ageing Soviet airport and Aeroflot's main hub in Russia.
In a statement, Aeroflot said it would study the inquiry results, but it dismissed the breaches as "insignificant" and added it would appeal against several conclusions.
"Aeroflot believe that these insignificant breaches... cannot affect flight safety. The hasty announcement by the prosecutor's office representative... does not reflect the actual state of the company's system of air safety.
"Such unfounded statements not only have a serious commercial impact on Aeroflot and Russian aviation but also damage Russia's authority as a member of the international aviation community," the statement said.
An Aeroflot jet flying from the airport in Moscow to the Urals region city of Perm crashed on September 14 as it was coming in to land, killing all 88 people on board. Investigators have blamed the crash on technical faults.
AFP