Former southern rebel leader Garang, who became Sudan's vice-president on 9 July after a peace agreement, had been reported missing in bad weather on Sunday on a flight from Uganda.
Late on Sunday state television interrupted its regular programing to say that Garang had "landed safely at a camp in southern Sudan".
A source in Garang's Sudan People's Liberation Movement, reached by phone in Nairobi, said Garang was safe. "Dr Garang is fine," the source said, but gave no further information.
But in the early hours of Monday morning, Sabdarat went on television to deny such reports.
"Up to now we do not have any concrete new information about the whereabouts of the plane," said Sabdarat, who is also the government spokesman.
"Now we are intensifying efforts to search and find out where it landed... We hope it landed somewhere safe," he said.
He also said the aircraft left Uganda on Saturday evening, contradicting earlier reports that it had gone missing on Sunday.
He said President Omar al-Bashir had ordered the Sudanese air force to search for the aircraft.
"Up to now we do not have any concrete new information about the whereabouts of the plane"
Abdel-Basit Sabdarat, information minister
"Sudanese President Omar al-Bashir contacted his Ugandan counterpart Yoweri Museveni to try and locate the aircraft carrying the first vice-president," state television said, reading a statement from al-Bashir's office.
Garang played a key role in reaching the peace deal earlier this year, ending 21 years of civil war that killed more than two million people.
State television had initially reported that air traffic controllers had lost contact with Garang's aircraft on its way from Uganda.
According to a senior Ugandan official, the Sudanese television report that Garang had landed safely was incorrect and a search would continue on Monday.
"The report that he landed at an army base in southern Sudan is wrong," the official said on condition of anonymity.
Garang had been in Uganda to meet with Museveni. The official said Garang and his entourage left Museveni's ranch in the western Ugandan town of Rwakitura in a Ugandan government helicopter on Saturday during daylight.
At some point during the flight they encountered bad weather and tried to go around it. Radio contact was then lost and it is unclear what happened to the helicopter.
An accident involving Garang would be a severe blow to the country's peace process. Under the January accord which ended the 21-year civil war, Garang was made first vice-president.
Crowds greeted his arrival in Khartoum.