Garang was flying back to Sudan from Uganda, where he had been meeting with Ugandan President Yoweri Museveni.
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 former leader of rebels in southern Sudan, Garang fought 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.
The helicopter was reported missing Sunday.
The government in Khartoum first made statements Sunday that Garang's aircraft landed safely. On Sudanese state television, a government spokesman later backtracked and said that there was no immediate information about the helicopter's whereabouts.