Some have been buried already as per Islamic rites, TV3 has gathered.
Five other Ghanaian pilgrims who died through natural causes have also been buried.
He said the bodies of some of the dead in the stampede was mutilated to the extent that it was difficult to fly them back home.
Alhaji Amin Lamptey, however, indicated that efforts to find about 25 missing Ghanaians have not abated though pilgrims have begun returning home.
The first batch of pilgrims touched down in Accra on Monday afternoon with the second and third already in the country.
Nine more flights are expected to carry the fresh Alhajis and Hajias into the country, Amin Lamptey said.
The Pilgrims Affairs Office last week published the names of Ghanaian victims of the deadly September 24 stampede.