The ministry said the troops, from 1st Battalion The Royal Anglian Regiment, were patrolling northwest of Kajaki in Helmand province on Thursday evening when they were attacked by Taliban insurgents.
The ministry said that "during the intense engagement that ensued, close air support was called in from two U.S. F15 aircraft to repel the enemy. One bomb was dropped and it is believed the explosion killed the three soldiers. "
The military did not identify the soldiers but said next of kin had been informed.
It said an investigation would be held into the incident.