The all-male victims, from countries in Africa, Asia and South America, were placed in institutions "under the protection of the state", the SEF said.
Two Portuguese nationals and five companies are under investigation in the operation launched Monday and christened "El Dorado" and which has seen several "passports and residency permits" seized.
According to local media reports, the victims were held in buildings belonging to the Bsports football academy in Riba d'Ave.
The wannabe footballers will give testimony before a judge before being repatriated to their country of origin.
One of the people under investigation was identified in media reports as Mario Costa, one of the officials behind the Bsports academy and president of the general assembly of the Portuguese football league, a post from which he resigned on Wednesday without admitting to any wrongdoing.
The illegal recruitment of footballers is "unacceptable and shocking," Portugal's Secretary of State of Youth and Sports Joao Paulo Correia said, adding that government would "take measures" to battle this type of human trafficking.
Portugal Finds, Frees Young Footballers
FILE: In this May 31, 2014 photo, a player controls a ball during a game of "altinho," where the goal is to keep the ball airborne while passed amid players.
LISBON — 47 young footballers, including 36 minors, have been rescued by Portuguese police in a crackdown on human trafficking linked to a training camp in the north of the country, the Immigration and Borders Service (SEF) said Thursday.