The family is still waiting for DNA results to confirm the body's identity.
Seen as Africa's Che Guevara, the anti-imperialist revolutionary was hastily buried in a 1987 coup.
Permission for an exhumation was denied during the 27-year rule of his successor Blaise Compaore, who was ousted in an uprising last year.
Mr Compaore has always denied being involved in the ex-leader's killing, insisting that the "facts are known" and he has "nothing to hide".
While he was in office, a Burkina Faso court blocked a request by Mr Sankara's family for his remains to be exhumed.
That changed last year when a transitional government came in after street protests.
The exhumation started in May but the autopsy report was delayed during last month's seven-day coup.
Ambroise Farama, one of the lawyers representing the Sankara family, said that the revelations about Mr Sankara's body were "mind-boggling", the AFP news agency reports.
"You could say he was purely and simply riddled with bullets," he said.
Autopsies on the other 12 soldiers buried with him in 1987 revealed they had only one or two gunshot wounds.
"But as far as Thomas Sankara was concerned, there were more than a dozen all over the body, even below the armpits," Mr Farama is quoted as saying.
Soldiers linked to Mr Compaore were behind last month's putsch, which delayed presidential elections due last Sunday.
Burkina Faso's interim government has now rescheduled the poll for Tuesday 29 November.
Who was Thomas Sankara?
AFP- A captain in army of Upper Volta, a former French colony in West Africa
- Instrumental in the coup that ousted Col Saye Zerbo as president in 1982
- Took power from Maj Jean-Baptiste Ouedraogo in an internal power struggle and became president in August 1983
- Adopted radical left-wing policies and sought to reduce government corruption
- Changed the name of the country from Upper Volta to Burkina Faso, which means "the land of upright men"
- Killed in mysterious circumstances by a group of soldiers in October 1987, aged 37
"The art of living consists of knowing what to pay attention to and what to ignore." -- Mardy Grothe