The four Haddad brothers were among 13 people arrested on Friday in one of the biggest raids since the 11 March 2004 attack.
On Tuesday, one of the brothers, Muhammad Haddad, was ordered to appear at a court once a week while police carry out further investigations, a court official said.
The other three were freed without restrictions.
Later on Tuesday, National Court Judge Juan del Olmo was to question the other nine people arrested in the raid and decide whether to release them or file terrorism-related charges.
The 13 were arrested on suspicion that they took part in preparations, such as logistics and recruitment tasks, before the bombing of the four commuter trains.
The bombings, Spain's worst terrorist attack, killed 191 people.
The Haddad brothers had been accused of having close links to a Moroccan man believed to be an al-Qaida spokesman.
His name was mentioned in a video showing fighters saying the network was behind the Madrid bombings.
The nine others are alleged to have links to a Tunisian man, Sarhani bin Abd al-Majid Fakhat, who was one of seven key Madrid bombing suspects who killed themselves and a Spanish policeman on 3 April last year by setting off a bomb as police moved in to arrest them.
Twenty-five people, most of them Moroccan, have been jailed on provisional charges in connection with the Madrid bombings. More than 60 other detainees have been released, but are still considered suspects.