Ministry spokesman Zemeri Bashary said rescuers had recovered a total of 157 bodies from the Salang Pass, a key road that connects the Afghan capital with the north.
Meanwhile, the army said rescuers recovered 39 bodies from the area on Wednesday, while another 29 bodies were recovered from the site on Tuesday.
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"We have recovered 39 bodies from two locations and more bodies from another location along the Salang Pass," said General Ahmad Zia Yaftali, chief doctor in the Afghan army.
Another 29 bodies were recovered from the site, in the Hindu Kush mountains, on Tuesday, the doctor said.
Yaftali told Agence France-Presse that an unknown number of bodies were recovered from a third location along the pass, and 16 survivors were rescued and evacuated.
A series of multiple avalanches that began Monday along the 3,800-metre pass closed off roads and stranded hundreds of people in snow-bound vehicles.
About 150 Afghan army personnel backed by bulldozers, digging machines and helicopters were conducting the rescue operation, Yaftali said, adding that avalanche snowfall on the road was hampering the risky operation.
Bashary said 2.5 kilometres of road had been cleared for emergency ambulances, bulldozers and other road-clearing equipment to get through.
About 2,600 people had been rescued so far.
