The United Nations' humanitarian agency said Wednesday it was scrambling to get emergency shelter, trauma care and food aid to the scene of a deadly earthquake in Afghanistan.

The earthquake struck a remote border region of Afghanistan overnight killing at least 1,000 people and injuring hundreds more, with the toll expected to rise.

The UN Office for the Coordination of Humanitarian Affairs (OCHA) said in its first response bulletin that humanitarian partners were preparing to assist affected families in Paktika and Khost provinces, in coordination with the Taliban authorities.

"Immediate needs identified include emergency trauma care, emergency shelter and non-food items, food assistance and WASH (water, sanitation and hygiene) support," OCHA said.

"Given the unseasonable, heavy rains and cold, emergency shelter is an immediate priority."

The 5.9-magnitude quake struck hardest in the rugged east, where people already lead difficult lives in a country in the grip of a humanitarian disaster made worse by the Taliban takeover in August 2021.

OCHA said the Taliban's disaster management and humanitarian affairs office had delivered food and emergency tents to some families living in the open but further help was needed.

The agency said the Afghan defence ministry had dispatched five helicopters to Paktika province to facilitate medical evacuations, while a medical team has been sent to Gayan district.

"Although search and rescue efforts are ongoing, heavy rain and wind is hampering efforts with helicopters reportedly unable to land this afternoon," said OCHA.

"The number of casualties is expected to rise as search and rescue operations are ongoing.

"Humanitarian search and rescue teams... are on standby to deploy as needed."

UNICEF, the UN children's agency, has also deployed at least 12 teams of health workers to Gayan, and several mobile health and nutrition teams to Barmal district in Paktika province and Spera district in Khost province, OCHA said.

Meanwhile the World Health Organization has also delivered 100 cartons of emergency medicine to Gayan and Barmal.

Up to 1,800 homes have reportedly been destroyed and damaged in Gayan, representing 70 percent of the district's housing stock, said OCHA.