The 16-year-old died after a seizure at the family's holiday home on New Year's Eve.
It is thought trained pilot John will fly the remains back to Ocala, Florida, on his personal plane.
At a news conference, funeral home director Keith McSweeney confirmed Jett's remains were being cremated.
'There is a lot of grief, a lot of pain, a lot of tears,' said Bahamian lawmaker Obie Wilchcombe, a friend of the Travoltas.
'John and Kelly are two crying human beings, not movie stars.'
The couple also have an 8-year-old daughter, Ella.