Colombia's President Juan Manuel Santos Tuesday ordered an investigation into allegations an army intelligence unit spied on his negotiators holding peace talks with the FARC rebel group.

Santos called the alleged eavesdropping an attempt by "obscure forces" to sabotage his efforts to end the half century old insurgency, denouncing it as "totally unacceptable."

He said he had instructed Defense Minister Juan Carlos Pinzon "to investigate this situation in depth: how far it reached, who was behind this, who was interested in taping our peace negotiators."

He said he wanted to know "what dark forces are behind this, if there are loose cannons in army intelligence, who they are reporting to."

The alleged spying was first disclosed by the magazine Semana, which reported Tuesday that a special army unit was set up in 2012 to illegally intercept the communications of members of the government's negotiating team.

The government's delegation to the peace talks in Havana is led by former vice president Humberto de la Calle, Sergio Jaramillo and Alejandro Eder.

Santos said the state had an obligation to spy on enemies like the FARC, or organized crimes.

"What is unacceptable from any point of view is that intelligence target legitimate, ordinary citizens, political opponents and much less officials of the state itself," he said.

In Havana, de la Calle declined to comment on the Semana report. A FARC delegate, Victoria Sandino, said the rebel group would make a statement on Wednesday.

"We knew there was spying, that's obvious," a member of the Farc delegation said, speaking on condition of anonymity.

"The news here is that a sector of military intelligence was spying on the presidency."

An official in the Colombian attorney general's office told AFP that an investigation has been underway for several weeks.

"Ten days ago the attorney general's office conducted a raid in Bogota and found computer equipment that is being examined by technical investigators," he said, speaking on condition of anonymity.

In 2011, Santos disbanded an intelligence agency, the Administrative Department of Security, which was involved in the alleged illegal wiretapping of leftist politicians and was said to have links to right-wing paramilitary groups.

Since November 2012, his government has been in negotiations with the FARC, the country's largest guerrilla group, aimed at ending an insurgency that has been waged since 1964.