Defense Minister Juan Carlos Pinzon said the hostages were killed during a mission to free them. He said all four men were shot; three with shots to the head and one with two shots to the back.
Among them was the longest-held captive, Sergeant Major Jose Libio Martinez, who was seized by the rebels almost 14 years ago.
Colombian President Juan Manuel Santos said the murders were another demonstration of the FARC's cruelty. He called the killings "an atrocious crime."
Troops launched the operation in southern Caqueta province 45 days ago after a tip that the captives were being held in the area.
The incident took place less than two weeks after FARC rebels named Timoleon Jimenez, better known as Timochenko, as their new leader.
Timochenko replaced former FARC leader Alfonso Cano, who was killed November 4 in a battle with government troops. Cano had led the group since 2008.
FARC rebels have been at war with the Columbian government since the 1960s. Their numbers have dwindled over the years, but some analysts estimate the group has as many as 9,000 fighters.
Most of FARC's funding comes from cocaine trafficking and extortion, but the leftist rebels are believed to be holding at least 14 people for ransom or political leverage.
FARC has been designated as a terrorist organization by Colombia, the United States and the European Union.
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