Febri Diansyah, a spokesman for the anticorruption agency, told reporters that the arrest warrant had been issued because of Mr. Setya’s status as a suspect in the identification card corruption case. “Our team is continuing to carry out the investigation,” he added.
It was unclear, however, how long Mr. Setya, who was being held at the K.P.K.’s headquarters in Jakarta, would remain in detention or whether he would go to trial.
In a pretrial hearing in late September, a Jakarta district court judge had cleared Mr. Setya as a suspect in the graft scandal, ruling that evidence and testimony against him that had arisen from the cases of other suspects in the scandal were inadmissible.
Amid an outcry from antigraft activist groups, the anticorruption agency gathered new evidence and renamed him as a suspect this month.
Mr. Setya’s defense team said it would immediately file a pretrial motion to clear Mr. Setya as a suspect, and said that his arrest violated Indonesian law and international human rights norms, given that he was in ill health.
For months, Mr. Setya missed appearances at the anticorruption agency to undergo questioning as a suspect. During that time, he was hospitalized twice: once for symptoms of vertigo after playing table tennis and for liver and heart ailments, and then last Thursday, after the reported car accident.
Photographs of him lying in a hospital bed on both occasions circulated on social media but were criticized by many in Indonesia as being faked.
Mr. Setya cut his political teeth in the Golkar party of Suharto, the autocratic former president, who by one estimate stole up to $35 billion during his 32-year rule before being toppled by pro-democracy demonstrations in 1998.
Currently Golkar’s chairman, Mr. Setya has been accused but never prosecuted in several corruption scandals. In one notable case in 2015, Mr. Setya was forced to resign as House speaker after an audiotape surfaced that purported to show him trying to extort billions of dollars in shares from the Indonesian unit of the United States mining giant Freeport-McMoRan. He was reinstated as speaker the next year.
Golkar is also a member of the governing coalition of Indonesia’s president, Joko Widodo. Mr. Joko, however, has taken a tough stance against corruption since his election in 2014 and is widely considered beyond reproach.
Mr. Setya’s prosecution would be one of the highest-profile corruption trials in the history of Indonesia, which according to various international surveys remains one of Asia’s most graft-ridden nations.
“No one should be above the law, least of all public officials and politicians,” said Natalia Soebagjo, a member of the board of Transparency International, a Berlin-based organization that monitors and publicizes corporate and political corruption.
“The way Setya Novanto has made a mockery of our legal system and of the public’s trust, we need to show that there is no more room for the likes of him,” she said.