The port fell to the hands of Taliban militants late on Wednesday night.
In a statement released on Friday, MoI said that Afghan forces have launched a joint clearance operation in the area.
According to the statement, Ay-Khanoom port is under control of the Afghan forces and the port is cleared of insurgents.
The operation will continue to clear Dasht-e Qala district from the Taliban militants.
The Taliban suffered heavy losses during the military operation, the statement added.
In a separate incident, a Taliban key commander was killed and three insurgents were wounded in clashes with the Afghan security forces in Chah Aab district of the province, Takhar police said.
Khalil Asir a spokesman for Takhar police told Ariana News that the incident took place on Saturday morning in Pai Shah village in Chah Aab district.
The Taliban commander was identified as Mullah Hashem.
Taliban militant group has not made a comment about the incidents so far.
Source : Afghan Voice Agency(AVA)