"We had 14 people on board [the helicopter]," Sam Kutesa, Ugandan foreign minister, told IRIN on Sunday night. "Six were Sudanese and eight Ugandans. We are still searching."
In Khartoum, the official Sudanese television reported on Monday that the helicopter had "crashed after hitting the Imatong Mountain chain in southern Sudan".
The Sudanese council of ministers was on Monday due to hold an emergency session to discuss the implications of the incident. Sudanese President Umar al-Bashir also met leaders of the Sudan People's Liberation Movement/Army (SPLM/A) in Khartoum.
A statement issued at 1:00 am (2200 GMT) on Sunday by Ugandan President Yoweri Museveni's office said Garang, who had been visiting Museveni's ranch in western Uganda, was flying in a Ugandan presidential MI-72 helicopter.
The statement said: "Garang left Rwakitura [Museveni's ranch] by presidential helicopter at 1545 hours (1245 GMT) for his base in southern Sudan, just north of Kidepo national park [...]. It [the helicopter] attempted to land in New Kush but aborted landing because of bad weather and headed southwest.
"Since morning we have been searching the Kidepo area to locate the plane without success," it added. "The governments of Sudan and Kenya have been informed. We do share the anxiety with the public since it is now 24 hours beyond the estimated time of arrival of the plane at its destination."
Garang, the chairman of the former southern rebel SPLM/A, signed a historic peace accord with the Khartoum government in the Kenyan capital, Nairobi, on 9 January to end more than two decades of war in southern Sudan.
On 8 July he was sworn in as new Sudanese First Vice President as well as President of southern Sudan to serve for a six year transitional period.
After the six years, a referendum would be held to decide whether southern Sudan should remain part of Sudan or break away to form its own state.
In April, a donors meeting in Oslo, Norway pledged more than US $ 5 billion for the reconstruction of southern Sudan. UN Secretary-General Kofi Annan applauded donors for their generous pledges.
An analyst in Nairobi said the helicopter incident could throw the entire southern Sudan peace process into jeopardy given that Garang had played a key role in the process.
An aid worker in southern Sudan said people in the region had initially reacted with "shock" to reports of the helicopter crash.