Rescuers have so far pulled two women's bodies from the rubble of the landslide in Baghlan province, said provincial Gov Abdul Majid.
The UN confirmed one other death and said houses were destroyed across five districts.
A massive landslide of mud and rocks buried houses so deep in the remote mountain village of Sayi Hazara that rescuers gave up trying to use shovels to dig through the buried buildings, said Jawed Basharat, a spokesman for the provincial police chief who was part of a team that examined the village after the slide.
There were no visible signs of the buildings underneath. "We need bulldozers or other machinery to remove all this earth and get the bodies out, or the survivors if there are any," Basharat said.
They knew how many houses were buried only from information provided by area residents, who said between 25 and 30 houses disappeared in the landslide.
An earthquake measuring a magnitude 5.4 struck the Hindu Kush region this morning, followed by a 5.7 quake, the US Geological Survey said. Both were felt as far away as the Afghan capital, Kabul, where buildings shook.
Baghlan province's Burka district, the site of the landslide, is a remote collection of mountain villages. It takes more than two hours to drive the approximately 40 kilometers from the provincial capital of Pul-e-Khumri to the area.