Carlos Alfonso Negret has urged Columbian authorities to protect civilians from violence during protests.
The FARC is preparing to demobilise under the accord but said its members had clashed with a breakaway group opposed to the agreement.
The unrest threatens to disrupt the FARC and government efforts to end their half-century-old conflict.
Ombudsman Carlos Alfonso Negret said various incidents had been reported in the south which posed a threat to civilians.
He said a woman was killed when regular FARC forces attacked a group led by a renegade commander.
The FARC earlier reported a clash last week in which it said one member of the breakaway group was killed.
The government warned in a statement that those involved in fighting at this stage in the peace process will not be covered by an amnesty included in the peace deal.