FARC rebels resumed peace talks with the Colombian government in Havana Monday after a brief pause in reaction to a proposal that any deal be put to a national referendum.

The Revolutionary Armed Forces of Colombia rejected President Juan Manuel Santos' proposal as a "flagrant violation" of agreements that led to the peace talks, but decided to resume discussions anyway.

"Despite the circumstances, the FARC will remain at the table, faithful to the commitment to search for peace for Colombia through all means," lead FARC negotiator Ivan Marquez said.

However, he said the government cannot unilaterally set forth the mechanism for giving legal standing to a peace agreement, should one be reached.

"To assume these powers is a flagrant violation of the general agreement signed in Havana," he said.

The proposed referendum "is not binding, we do not go along with it, nor will we base the dialogue and the outcome on this unilateral decision," he said.

Santos surprised the rebel group Thursday by submitting legislation to Congress stipulating that any peace agreement must be put to a national vote, either in legislative or presidential elections next year.

Legislative elections are due in March 2014, and the presidential poll is set for May.

The following day the FARC, Colombia's largest guerrilla group, announced a pause in the talks so it could analyze the implications of a referendum.

The FARC had called for the creation of a national constituent assembly as a forum to ratify a peace agreement.

Marquez reaffirmed that position on Monday, adding: "Once and for all, the FARC will not submit itself to any legal framework of a unilateral design."

Despite the FARC's vehement response, analyst Leon Valencia, head of the Peace and Reconciliation Foundation, said the incident was now over.

"The government was thinking about presenting the referendum bill in the talks in Cuba, but the news leaked and that's why Santos announced it," he said.

"The government has made a positive assessment of the way the peace talks are developing and believes that (an agreement) could be ready before the end of the year," he said in Bogota.

The sides have made some progress since the Havana talks began in November, but they are less than halfway through a five point agenda.

The FARC, which has an estimated 8,000 fighters, has been waging an insurgency against the state since 1964, making it the longest armed conflict in Latin America.

One of the Marxist-inspired group's front leaders, Virgilio Vidal Mora, alias Silver, was killed in an army bombing raid on Monday in the western Colombian department of Choco.