The southern battle - fought by Afghan soldiers aided by NATO air strikes - took place in Sangin, Helmand province. Sangin neighbors Musa Qala, which Taliban fighters had controlled since February but abandoned this week in the face of an offensive by Afghan, British, and US forces.
"When the terrorists were defeated in Musa Qala, they escaped to Sangin and started firing in and around Sangin," the Defense Ministry said. Among the 50 militants killed were three foreigners and three commanders, the ministry said. It said no civilians were hurt.
There was no way to verify the death toll independently at the remote battle site, and NATO officials do not release casualty figures for militants.
Taliban militants overran Musa Qala in February, four months after British troops left the town following a contentious peace agreement that gave security responsibilities to Afghan elders, a deal criticized by US officials as surrendering to the Taliban.
Afghan, British, and US forces moved into Musa Qala's center on Tuesday. More than two dozen militants were killed in the battle for Musa Qala, as was one British soldier.
Helmand Governor Asadullah Wafa said he and a delegation of officials from Kabul would travel to Musa Qala today to hand out 5,000 tons of aid, including wheat and blankets, to families who fled the fighting and are now starting to return.