"The court brought in a non-guilty verdict based on the jury's acquittal decision," Anna Usachyova said.
Usachyova said eight of the 12 jurors had found the suspects not guilty of the murder of Igor Klimov. The general director of the Almaz-Antei consortium was shot dead in June 2003 outside his home in central Moscow.
Konstantin Bratchikov and Stanislav Tyurin, who were accused of organizing the murder, had previously been acquitted, but the Supreme Court overruled the decision and ordered a new trial.
Bratchikov and Tyurin had earlier also been charged with involvement in the murder of Yelena Neshcheret, the head of industrial tools manufacturer Prommashininstrument, on October 9, 2003.
Investigators said Klimov and Neshcheret had been killed over the redivision of commercial interests.
Klimov's killers were sentenced to 20 and 25 years in prison in 2006. Yevgeny Mankov, the leader of a six-member gang behind Klimov's murder was sentenced to life in October of 2005, but a year later his sentence was reduced to 25 years.
Before his appointment as head of Almaz-Antei in August 2002, Klimov - who lived in St. Petersburg with a background in foreign intelligence - had worked in the presidential administration under Vladimir Putin.
The Almaz-Antei company specializes in developing and producing small, medium and long-range air defense missile systems, radars and automated control systems.