Court spokeswoman Anna Usachyova said eight of the 12 jurors found the suspects not guilty of the 2003 murder of Igor Klimov.
Konstantin Bratchikov and Stanislav Tyurin, who were accused of organizing the murder, had previously been acquitted, but the Supreme Court of Russia overruled the decision and ordered a new trial.
Klimov, general director of the Almaz-Antei consortium, was shot dead in the morning of June 6, 2003, outside his home in central Moscow.
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.
Klimov's killers were sentenced in 2006 to 20 and 25 years in prison. Yevgeny Mankov, the leader of a six-man 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 - a resident of 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.
