Before his release last Monday, the 69-year-old had been in jail since his arrest in 2016, two months after an attempted coup which Ankara says was orchestrated by the network of U.S.-based Muslim cleric Fethullah Gulen.
The journalist's case has drawn criticism from human rights groups and Turkey's Western allies. They are concerned by the scale of a post-coup crackdown against suspected Gulen supporters under President Tayyip Erdogan.
Altan smiled and waved as he was driven away by counter-terror squad police officers after being taken from his home in Istanbul, video and photos published by Turkish media showed.
He was taken to Istanbul police headquarters after a hospital check-up, state-owned Anadolu news agency reported.
Altan, his brother and other journalists were previously sentenced to life in jail for aiding Gulen's network. Last week he was convicted again in a retrial, but released from jail given the time served.
Altan and the others deny the charges against them.
On Tuesday a higher court overruled the decision to release Altan, ordering his arrest on grounds that there was a risk of him fleeing, Anadolu reported.
Under last week's verdict, Altan was sentenced to 10 years and six months in jail. Turkey's high court had overruled the previous life sentences against him in July, sending the file back for re-trial.
Erdogan's government has jailed more than 77,000 people pending trial since the failed putsch. Widespread arrests are still routine in a crackdown critics say demonstrates growing autocracy in Turkey.Gulen, who has lived in self-imposed exile in Pennsylvania since 1999, and his followers deny any involvement in the coup. Turkey has repeatedly called on the United States to extradite the cleric.