"The cortege with the body is being flown by Emirates Airlines to Bengaluru. It will be taken to Mysuru in a special aircraft," the official told IANS.
Siddaramaiah, his wife Parvathi, their daughter-in-law and younger son Yathindra are accompanying the cortege.
Rakesh, 39, died of multi-organ failure on Saturday at Antwerp University Hospital in Brussels.
Rakesh was undergoing treatment for a pancreatic ailment at the hospital where he was admitted after developing sudden health complications when he was on a personal trip to Europe with friends since July 21.
The Chief Minister's family has appealed to the public, relatives and friends not to assemble at the Bengaluru airport.
Mysuru, about 150 km from Bengaluru, is the hometown of Siddaramaiah. He represents the Chamundeshwari assembly segment in the district as lawmaker of the ruling Congress since May 2013.
The body will be taken to Siddaramaiaha's farm house on the outskirts of Mysuru for the last rites in the evening.
Meanwhile, Siddaramaiah expressed gratitude to people, especially friends and well-wishers, for standing by him.
"My pain is inexplicable and my loss is irreplaceable. Still, I am unable to hold back tears. I will be failing in my duty if I do not express gratitude to all the people, who stood by me in this hour of grief," said Siddaramaiah in a message from Brussels before he left for India.