According to the statement, the soldier was wounded in the buttocks by a shrapnel from a rocket-propelled grenade.
After receiving medical attention in a Kandahar hospital, the soldier was returned to the camp at the city airport and is feeling well, the ministry said.
The soldier was injured during a routine patrol and he is the first Croatian serving in Afghanistan to be wounded.
The attack occurred during a visit by Croatian Defence Minister Berislav Roncevic to Afghanistan.
Croatia has been participating in the ISAF mission since 2003. The Croatian contingent has 150 troops deployed in different locations in the country.