NAIROBI—Nearly all United Nations road and air shipments have been halted in South Sudan, officials said Thursday, after South Sudanese forces discovered mislabeled weapons sent to rebel-held parts of the country.

Since the weapons were discovered in Rumbek last week, South Sudan's troops also are restricting the movements of peacekeeping forces, said Ariane Quentier, a spokeswoman for the U.N. mission in the country. The incident has inflamed tensions between the U.N. and South Sudan's government, and halted much of the international organization's humanitarian work in the country.

"It is important that the investigations clear this as soon as possible such that we resume our activities without any hindrance," Ms. Quentier said.

On Thursday, South Sudanese government troops battled rebel fighters for control of Malakal, the capital of the oil-producing Upper Nile state. Also, East African mediators said they would deploy a regional force to preserve a now tattered cease-fire deal from January.

The U.N. has been struggling to provide assistance in contested areas to about 4.9 million civilians estimated to need food or other help.

That effort hit a big roadblock last week after the South Sudanese government accused the U.N. of arming rebel factions. It said its forces found weapons and ammunition in shipping containers labeled "general goods" aboard U.N. trucks headed to the north of the country. The U.N. has said the weapons were meant for its peacekeepers and were accidentally mislabeled.

Shipments of humanitarian supplies, such as food and medicine, have been stalled in the wake of the incident. "In the past week our logistics operation has essentially ground to a halt," said Challiss McDonough, a regional spokeswoman for the U.N.'s World Food Program. She said other U.N. trucks had been similarly blocked.

South Sudan's information minister said that all road shipments were being searched but that there had been no order to block shipments from proceeding.

"There is no shipment that hasn't been allowed to move," Michael Makuei Lueth said. He said the South Sudanese government also had done nothing to limit U.N. patrols or any other peacekeeping operations.

However, he also said the South Sudanese government didn't accept the U.N. explanation and believed it was trying to arm rebels. He said all such shipments into South Sudan are checked on arrival by both South Sudanese and U.N. officials. Mr. Lueth said that if the containers had been mislabeled at their origin, the mistake would have been discovered then. He said U.N. staff in South Sudan must have relabeled them.

"We don't believe that it was an accident," Mr. Lueth said. "We have no problem with the United Nations…We have problems with the personnel running the offices of the U.N. here."

The dispute is the latest tense moment between the U.N. and the South Sudanese government. At the onset of fighting in December, the government accused the U.N. of letting rebels shelter in its bases. And in January, President Salva Kiir accused the U.N. of overstepping its mandate after peacekeepers blocked security officials from accessing a U.N. base in the town of Bor. U.N. officials denied the first allegation and said it blocked the security officials because they were carrying weapons.

Write toandnbsp;Heidi Vogt in Nairobi atandnbsp;heidi.vogt@wsj.comandnbsp;and Nicholas Bariyo in Kampala atnicholas.bariyo@wsj.com

Corrections andamp; Amplificationsandnbsp;
The first name of Ariane Quentier, a spokeswoman for the U.N. mission in South Sudan, was incorrectly given as Arian in an earlier version of this article.