Air traffic controllers in Khartoum lost contact with the aircraft on Sunday amid reports that it had crash landed in southern Sudan.
Earlier reports said the helicopter carrying the former rebel leader, who recently joined a government of national unity, went down in southern Sudan, an army official said on Sunday.
Ugandan troops had been searching for Garang. Garang is now said to be safe at a military base in southern Sudan, Sudanese television reported.
Ugandan army 2nd Captain Dennis Musitwa said the helicopter apparently went down in bad weather during a return flight from Uganda, once a supporter of Garang's southern rebels.
The Uganda army spokesman said Garang was on a private visit in Uganda, which has pledged to repair relations with Sudan now that peace has been declared in the southern war.
"They left yesterday in a Ugandan chopper," Musitwa told The Associated Press. "What we know is that the aircraft got weather problems and crash-landed.
"We have not established where they landed. They have not reached where they are supposed to reach, and we are trying to locate them," he said.
A spokesman for Garang's Sudan People's Liberation Movement said in Kampala that Sudanese officials had no communication with Garang or the helicopter.
"What I've heard is that the plane encountered some weather problems and the pilot failed to fly it back to Uganda," party spokesman George Riek said.
"But at this point, we don't know what is happening on the ground, there are no communication links, no radios, nothing."
"What I've heard is that the plane encountered some weather problems and the pilot failed to fly it back to Uganda"
Sudan People's Liberation Movement spokesman
Earlier in Nairobi, Kenya, another party spokesman Yasir Arman said that Garang was "safe and sound" in southern Sudan. Arman declined to give further details, and there was no immediate explanation for the apparently conflicting report on Garang.
Garang is a charismatic figure whose leadership is seen as key to ensuring the deal ending 21 years of fighting in the south holds, and who could help bring peace to other volatile regions in Sudan, including Darfur.
Garang led the Sudan People's Liberation Army in the war between the Muslim north and mainly Christian and animist south that ended in January with the signing of the peace pact, which provided a power-sharing between the Khartoum government and Garang's movement.
The settlement made Garang first vice president - second only to President Omar el-Bashir - as well as president of southern Sudan, letting him set up an interim administration there until a referendum in six years on secession.