In an apparent case of identity theft, the Paris Saint-Germain star's name, date of birth and Brazilian ID number were used to register for the payment from the federal government, news site UOL reported.
The emergency payments are meant to help Brazilians employed in the informal sector whose jobs and incomes have vanished with stay-at-home measures to contain the virus.
Neymar's estimated earnings at PSG this year were $95.5m, after his record transfer of € 222m (Dh915m).
According to UOL, the application in his name "was initially approved and scheduled for payment... before being frozen and placed 'under evaluation' due to indications it failed to meet the requirements".
UOL reported that Neymar's staff said the Brazilian "obviously never applied for this benefit, and does not know who would have done so."
Brazil is one of the countries hit hardest by the coronavirus pandemic. It has the third-highest death toll globally, at more than 34,000, behind only the US and Britain.