Socrates, 57, has been held since his shock arrest at Lisbon airport on Friday, a first for a former leader of Portugal since its military dictatorship ended in 1974.
After lengthy questioning on Monday in connection with the corruption probe, a judge ordered the brash former Socialist leader be held in custody in a prison in the southeast of the country.
Socrates, who was prime minister from 2005 to 2011, has been placed under formal investigation suspected of "tax evasion, corruption and money laundering", according to the judge's statement read out to reporters.
Under "provisional detention", Socrates can be held for up to a year because his case is of "extreme complexity", although the investigating magistrate must reexamine his situation every three months.
Businessman Carlos Santos Silva and Socrates' chauffeur Joao Perna were also being held, while lawyer Goncalo Trindade Ferreira was freed on bail.
Searches have been carried out in recent days at business premises and Socrates' home in Lisbon.
Luis Montenegro, parliamentary leader of the ruling Social Democrats (PSD), said Portugal's image had been tarnished "both internally and abroad" by the probe.
Macedo resigned on Sunday over a money-laundering and influence-peddling scandal linked to a so-called "golden visa" programme, which gives residency permits to wealthy foreigners.
"Corruption is a serious problem in Portugal for political leaders because there are so many situations that involve conflicts of interest," Joao Paulo Batalha, a local representative for Transparency International, told AFP.
The centre-right government has said little about the corruption case.
Prime Minister Pedro Passos Coelho said Sunday that the probe "pertains to the law and not politics" and that Portugal "has strong institutions that work".
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