On Sudanese state television, a government spokesman said that there was no immediate information about the whereabouts of the aircraft. The government in Khartoum had made earlier statements Sunday that the copter landed safely.
The helicopter was flying from Uganda to southern Sudan when air traffic controllers in Khartoum lost contact. The area was under bad weather over the weekend.
A search was expected to be mounted on Monday.
Garang had been meeting with Ugandan President Yoweri Museveni before beginning the flight back to Sudan.
Garang is a former leader of rebels in southern Sudan, fighting with the Khartoum government for 21 years until signing a peace agreement in January. Under the terms of the peace deal, he was sworn in three weeks ago as Sudan's first vice-president and president of the south.