The ministry said the shooting at a base in the Nad-e Ali area of southern Helmand province claimed the life of a member of the Royal Scots Borderers, 1st Battalion the Royal Regiment of Scotland, the BBC reported.
Details of the shooting were not immediately available.
"This is incredibly sad news for the battalion and everyone serving in Task Force Helmand," Maj. Laurence Roche, spokesman for the British task force, was quoted as saying. "As we mark Remembrance this weekend, our thoughts now turn to the soldier's family and friends whose loss is so much greater than ours."
Such "green on blue" attacks by Afghans serving alongside coalition troops or by insurgent infiltrators in Afghan security uniforms have become a major security concern for U.S. and NATO forces as they occur despite tightened security.
The BBC said more than 60 coalition force soldiers have died so far this year in insider attacks. The foreign forces are scheduled to end combat operations and hand over Afghanistan's security to Afghan security forces by the end of 2014.