The U.N. earlier this week urged South Sudanese authorities to remove the new taxes, introduced in February. The measures applied to charges for electronic cargo tracking, security escort fees and fuel.
In its announcement Friday, the government said it was keeping charges on services rendered by firms contracted by the U.N. peacekeeping mission in South Sudan.
"These companies are profiting ... (and) are subjected to applicable tax," Finance Minister Awow Daniel Chuang said.
There was no immediate comment from the U.N. on when the airdrops could resume.
Earlier, the U.N. Humanitarian Affairs Agency said the pausing of airdrops had deprived 60,000 people who live in areas inaccessible by road of desperately needed food in March, and that their number is expected to rise to 135,000 by the end of May.
The U.N. said the new measures would have increased the mission's monthly operational costs to $339,000. The U.N. food air drops feed over 16,300 people every month.
At the United Nations in New York, U.N. spokesman Stephane Dujarric said the taxes and charges would also impact the nearly 20,000-strong U.N. peacekeeping mission in South Sudan, "which is reviewing all of its activities, including patrols, the construction of police stations, schools and health care centers, as well as educational support."
An estimated 9 million people out of 12.5 million people in South Sudan need protection and humanitarian assistance, according to the U.N. The country also has seen an increase in the number of people fleeing the war in neighboring Sudan between the rival military and paramilitary forces, further complicating humanitarian assistance to those affected by the internal conflict.