The legendary player allegedly mentioned his fellow countryman, the Manchester City striker, while commenting on the problem of players taking recreational drugs.
A spokesman for Robinho strenuously denied the suggestion as "absurd" and called for the World Cup legend to retract the remark.
Pele, 68, was allegedly recorded making his comments at a private event in Brazil.
The comments were picked up by the Brazilian radio station Jovem Pan and reported in newspapers and broadcasting outlets.
He allegedly said: "It's unfair to talk of drugs in football just because of one or two cases," before naming Robinho and another Brazilian star.
But a spokesman for the £32.5 million player said that Pele may have been misunderstood.
"The notion of him taking drugs is absurd and we completely deny it," a spokesman for the 25-year-old footballer said.
The club also emphasised that players undergo rigorous drugs tests regularly.
Born in the Sao Vicente slums in the town of Santos near Sao Paulo, the young player - whose full name is Robson de Souza - was once seen as an heir to Pele.
But he has been no stranger to controversy. During his time at Real Madrid, he fell out with Fabio Capello amid reports of drinking and partying in exclusive clubs.
He was questioned by British police in January following an allegation that he sexually assaulted a teenager in a nightclub in Leeds.
He strenuously denies the claim and was released on police bail without charge.