Garrincha, who was nicknamed 'the Joy of the People' for his brilliant performances on the right wing, won World Cups in 1958 and 1962 alongside players such as Pele and Mario Zagallo.
He died in 1983 after a long battle with alcoholism and was buried in his home town cemetery in Mage, around 40 miles from Rio de Janeiro.
News reports on Wednesday said his remains had been exhumed and there was no record of what happened to them.
"From our research, we're not sure he's still buried," a cemetery official told Rio’s Extra newspaper. "We have information that the body was exhumed and taken to a niche but there is no documentation about the exhumation."
Brazilian cemeteries are usually split into two sections, with tombs where bodies are buried and walls with drawer-like concrete niches where ashes or bones are stored.
The Raiz da Serra cemetery in Mage has two tombs with Garrincha's name on them.
One is a plot where Garrincha was originally laid in 1983 alongside other members of his family. The second is marked with an obelisk and was built in 1985.
The city mayor's office later issued a statement that said they had no precise record of where the player’s bones were but suspected they were in one of the two plots. The office stressed they were not lost.
“At no time did we say or did we believe that his mortal remains had gone missing,” the statement said.
“In the face of this doubt the mayor’s office has begun proceedings, in the public interest and of those of Garrincha’s family, to resolve this question once and for all.
“Therefore the municipality is looking to get the authorisation for an exhumation, for both the transfer of the genetic material necessary for an exam and (to find) the whereabouts of his mortal remains."
Officials are expected to ask Garrincha's family to provide DNA samples to help them confirm the bones in one of the plot's are Garrincha's.
Garrincha's daughter Rosangela Santos told Reuters that a gravedigger at the cemetery informed her that her father's remains were likely to be in one of the two graves.
"We don't know for sure where he is," she said. "The mayor has promised him a mausoleum but they need to find him first.
"It's very upsetting not knowing where he is."
(Reporting by Andrew Downie, editing by Ed Osmond)
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