A further 500 people were injured in Kunar province, the agency said.
The 6.0 magnitude earthquake struck the northeast, in the rugged, mountainous Jalalabad area close to the border with Pakistan at around midnight local time, officials said on Monday.
It was just eight kilometres deep. Shallower quakes tend to cause more damage.
Early reports showed 30 dead in a single village, the health ministry said, but added that accurate casualty figures had yet to be gathered in an area of scattered hamlets with a long history of earthquakes and flooding.
"The number of casualties and injuries is high, but since the area is difficult to access, our teams are still on site," health ministry spokesperson Sharafat Zaman said in a statement.
Hundreds of injured were taken to hospital, said Najibullah Hanif, the provincial information head, with figures likely to rise as reports arrived from remote areas with few roads.
Taliban government spokesman Zabihullah Mujahid said "sadly, tonight's earthquake has caused loss of life and property damage in some of our eastern provinces", in a post on X.
Rescuers were working in several districts of the mountainous province where the quake levelled homes of mud and stone on the border with Pakistan's Khyber Pakhtunkhwa region, officials said.
Jalalabad is a bustling trade city due to its proximity to Pakistan and a key border crossing between the countries.
Although it has a population of about 300,000 according to the municipality, its metropolitan area is thought to be far larger.
Most of its buildings are low-rise constructions, mostly of concrete and brick, and its outlying areas include homes built of mud bricks and wood. Many are of poor construction.
Afghanistan is prone to deadly earthquakes, particularly in the Hindu Kush mountain range, where the Indian and Eurasian tectonic plates meet.
A series of earthquakes in its west killed more than 1000 people last year, underscoring the vulnerability of one of the world's poorest countries to natural disasters.
A magnitude 6.3 earthquake struck Afghanistan on October 7, 2023, followed by strong aftershocks. The Taliban government estimated that at least 4000 people died.
The UN gave a far lower death toll of about 1500. It was the deadliest natural disaster to strike Afghanistan in recent memory.
with dpa and AP
