Portugal midfielder Kenedy was sent home from the World Cup on 22 May.
And Federation vice-president Amandio de Carvalho said that the player had been suspended as a precautionary measure as of Friday.
The suspension will be examined by the disciplinary commission of the Portuguese Professional Footballers league.
They will decide whether to open proceedings or take sanctions against Kenedy.
A Portuguese newspaper report on Wednesday claimed Kenedy also tested positive in February but the results were never reported.
And, after the test earlier this month, Portuguese football federation president Antonio Boronha defended the decision to send the player home immediately.
Kenedy was only named in the squad after Benfica's Simao Sabrosa and Luis Boa Morte of Fulham were ruled out with injury.
But he then failed a drug tests after taking a slimming pill that contained a banned substance.
"It was a very difficult decision to send the player away before the second analysis had proved positive," Boronha told the O Jogo newspaper.
"But it has to be understood that we couldn't run the risk of going to the World Cup with 22 players.
"Technically, tests are only positive after a second test but in 99% of cases they are found to be positive again.
"Sometimes it is hard but I believe we have made the right decision."
Kenedy was replaced in the Poretugal squad by Sporting's Hugo Viana.