It identified the journalist as Romeo Langlois, who has worked for the French newspaper Le Figaro, and said he was accompanying troops on an anti-drugs mission in the southern state of Caquetá.
The ministry said another four soldiers had been wounded in heavy fighting with the Revolutionary Armed Forces of Colombia, or Farc, during an operation by Counter-narcotics Batallion No 1 that destroyed five cocaine processing labs.
Langlois lives in Colombia, and the ministry identified him as a war correspondent. It did not say when the anti-drugs mission began.
Speaking on condition of anonymity, a senior police official said the fighting occurred on Saturday and that heavy rain in the area after nightfall was impeding military operations.
The defence ministry said that in addition to Langlois, four soldiers and a police officer were missing. The operation occurred in the hamlet of Buena Vista, in the municipality of Montanita.
Langlois is a freelancer with experience in the region and covering the Farc, an official with the French foreign ministry said. The official said Langlois had recently worked for the television news network France 24.
The official said the French government was in contact with Langlois's family as Colombian authorities searched for those missing. He said it was too early to release any further information.
The Farc, founded in 1964, is Latin America's last remaining major leftist insurgency. Funded largely by the cocaine trade, it has in recent years been seriously weakened by Colombia's US-backed military. It is believed to number about 8,000 fighters.
This month the Farc released what it said were its last remaining "political prisoners", after pledging to halt ransom kidnapping. It has been blamed for the kidnapping last June of four Chinese oil workers in the same southern state where Saturday's incident occurred.
