Rio de Janeiro police "have opened an inquiry to investigate whether the crime of violating a grave occurred", they said in a statement.
Garrincha, who was nicknamed 'The Joy of the People' for his brilliant performances, won World Cups in 1958 and 1962 alongside players such as Pele and Mario Zagallo.
He died aged 49 in 1983 after a long battle with alcoholism and was buried in his hometown cemetery in Mage, around 40 miles (65 km) from Rio.
However, reports earlier this week said his body had been exhumed from one of the two family plots that carry his name and a scandal has grown over the whereabouts of the beloved forward.
Local officials said they did not know if his bones were in one of the two graves and asked for permission to open them and take DNA samples to solve the mystery.
Police said they would investigate whether a crime was committed and warned that exhuming a body without the proper authorisation was punishable by up to three years in prison.
Garrincha played 60 times for Brazil and lost only once, but he was almost as famous for his colourful private life as for his brilliance on the field with Botafogo and the national side.
(Reporting by Andrew Downie; Editing by Andrew Bolton)
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