Edson Cholbi de Nascimento, who goes by his nickname of Edinho, was taken into custody in his home town of Santos, a coastal city where his father played for most of his career. Pele led Santos to two world club championships, while also helping propel Brazil to three World Cup triumphs.
A judge in the nearby beach town of Praia Grande ordered Edinho and six other people to be detained on drug trafficking and money laundering charges.
The arrest was not the first for Edinho, a 34-year-old former goalkeeper with the Santos club. He was arrested last June on charges that he had ties with a notorious drug trafficker. He spent almost six months in jail before being released in December. No trial date has been set.
Last July, he was cleared of manslaughter charges over his involvement in a 1992 car accident that caused the death of an elderly motorcyclist. That decision overturned a 1999 ruling that had found Edinho guilty but did not result in him being sent to jail.
Edinho has admitted that he has a marijuana habit but has denied any involvement with drug trafficking.
After being released from jail in December, he checked into a rehabilitation clinic at his father's urging.
Police, however, say they have recordings of telephone calls in which Edinho is heard negotiating how to invest money with a drug kingpin who has since been arrested.
Pele, who is widely considered the greatest football player of all time and is still a revered figure in Brazil, has stood by his son throughout the ordeal.
The former soccer great wept publicly when he visited Edinho in jail after his arrest last year.