It identified the missing journalist as Romeo Langlois, whose has worked for media including the Paris newspaper Le Figaro, and said he was accompanying troops on a counterdrug mission in the southern state of Caqueta.
In a statement, the ministry said four soldiers were also wounded in what it called "heavy combat" with the leftist Revolutionary Armed Forces of Colombia, or FARC, during an operation by Counternarcotics Batallion No. 1 that destroyed five cocaine processing labs.
Langlois is a Colombia resident, and the ministry identified him as a "war correspondent."
It did not say when the counterdrug mission began.
A senior police official said the combat occurred on Saturday and that heavy rain in the area after nightfall was impeding military operations. The official spoke on condition of anonymity because he was not authorized to provide information.
The Defense 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.
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 U.S.-backed military. It is believed to number about 8,000 fighters.
The FARC released earlier this month 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.