The US said "regional extremists" could target the flights
The US embassy in the Sudanese capital Khartoum has warned of a possible attack on Air Uganda planes.
The embassy said it had information that US travellers faced a potential threat between Juba in Sudan and the Ugandan capital, Kampala.
But the Sudanese foreign ministry said the threat was "not serious".
Sudan is on a list of 14 countries where US-bound passengers will be subjected to extra searches following the attempted plane bombing last month.
Other Sudanese officials said they had known of a potential threat for some time.
The AFP news agency reported that one plane en route to Juba was diverted as a precaution.
In a statement, the US embassy said it had "received information indicating a desire by regional extremists to conduct a deadly attack on board Air Uganda aircraft" on the Juba to Kampala route.
The embassy said the "capacity of these extremists to carry out such an attack is unknown" but that the threat was "of sufficient seriousness that all American air travellers should be made aware".
AFP said an Air Uganda flight was returned to Entebbe airport in Kampala when it was ordered to return.
Ignie Igunduura, a spokesman for Uganda's Civil Aviation Authority, said the information was not new and the authorities had "been aware of this threat for some time".
"But any time there is renewed information, and this renewed information came from the US but also others, you don't start taking chances," he said.
A spokesman for the Ugandan army, Lt Col Felix Kulayigye, also said he was surprised the US had issued the warning as the intelligence had been known since early December.
He said the country was "a constant target of these extremists" and was always on the alert, so there was "no cause for alarm".
But Foreign Ministry spokesman Moawiya Osman Khalid said there was nothing to support the allegations of a planned attack and criticised the US for the manner of the warning.
"They did not inform us of this security threat, we learnt about it from the embassy's website," AFP quoted him as saying.
"They did not ask for our cooperation, which they should have done before notifying the media."
The US has stepped up its air security after a Nigerian man allegedly attempted to blow up an airliner bound for Detroit on 25 December.
Umar Farouk Abdulmutallab - who allegedly tried to detonate explosives concealed in his underwear - has been charged with the attempted murder of 290 people and five other counts.