Three Taliban commanders were among those killed in the clashes, which saw Afghan forces being backed by the Nato-led International Security Assistance Force (ISAF) air force, the ministry said.
Among the dead were three foreign fighters, it said.
There was no way to independently verify the death toll on the remote battle site, and ISAF does not release casualty figures for fighters.
Battle for Musa Qala
Taliban fighters overran Musa Qala in February, four months after British troops left the town following a peace agreement that handed security responsibilities to Afghan elders, a deal criticised by US officials as surrendering to the Taliban.
Afghan, British and US forces moved into Musa Qala’s centre on Tuesday, and Afghan and British officials have vowed to station troops there and prevent it from again falling to the Taliban.
More than two dozen fighters were killed during the battle for Musa Qala, as was one British soldier.
Taliban fighters fled Musa Qala, but said they would continue their fight against security forces.
A spokesman said Taliban fighters had retreated to avoid civilian casualties in the attacks, but the Afghan army said that four civilians killed in the fighting had been used by Taliban fighters as human shield.
Asadullah Wafa, Helmand’s governor, said he and a delegation of officials from the Afghan capital, Kabul, would travel to Musa Qala on Thursday to hand out 5,000 tonnes of aid, including wheat and blankets, to families who fled the fighting and are now starting to return.
“After 11 months the Afghan flag is again flying over the Musa Qala district centre,” Wafa said.
The defence ministry said soldiers were now moving through the area, which is Afghanistan’s premier opium-growing centre, searching for remnants of the Taliban.
“The Afghan National Army and Nato troops are trying to secure the surrounding areas of the district,” the ministry said.
In a separate incident, a suicide bomber hit the centre of Kandahar, the main city in southern Afghanistan, killing a passer-by and wounding two Afghan army soldiers, security officials said.
Meanwhile, Isaf said two Nato soldiers were killed and three wounded when a convoy hit an explosive in eastern Afghanistan on Wednesday.
Isaf did not release the nationalities of the casualties from the blast which was caused by an improvised explosive device.
Around 218 foreign soldiers have been killed in Afghanistan this year, most of whom were killed in combat.