South Sudanese authorities are holding up United Nations fuel tankers over a tax dispute, jeopardising the delivery of millions of dollars of aid during a humanitarian crisis, the UN mission there said.

The trucks were held up at depots and the Ugandan border on Wednesday despite assurances from the minister of humanitarian affairs a day earlier that a new tax on trucks carrying fuel and other supplies did not apply to UN humanitarian operations, a spokesperson for the mission said.

Minister of Humanitarian Affairs Albino Akok Atak and Information Minister Michael Makuei were not immediately available for comment.

The trade ministry order this week, announcing the tax, said the $300 charge on each goods truck entering and leaving the country was intended to help the government maximise revenue collection by addressing undervaluations and fraud.

South Sudan, where hundreds of thousands of people died as a result of civil war from 2013-2018, is experiencing one of the world's worst humanitarian crises as a result of persistent conflict, natural disasters and poverty.

Last month, the United Nations estimated that about 7.1-million of its 12.4-million people would experience crisis-level hunger during the April-to-July lean season. 

"As of now, the trucks are still held up. The mission is continuing to engage intensively at the highest levels to resolve the situation," Priyanka Chowdhury, acting spokesperson for the mission, known as UNMISS, told Reuters.

Humanitarian airdrops have been suspended, affecting 60 000 people in need, and UNMISS has also been forced to review peacekeeping patrols and reduce support to peace and electoral processes, the mission said in a statement on Tuesday.

Traders and other organisations have protested against the measure and diplomatic missions called its imposition on UN and other aid operations “illicit and unacceptable” in a statement on Sunday.

UNMISS has around 20 000 peacekeepers who protect about 180 000 internally displaced people across the country.