Nezar Patria. Courtesy of Nezar Patria

JAKARTA, Indonesia—When Special Forces soldiers kidnapped Nezar Patria in 1998, tortured him and kept him in solitary confinement for three months, he wondered if he would survive. He never imagined his ordeal would someday figure in a presidential campaign.

The abduction of Mr. Patria and eight other pro-democracy activists was ordered by then-Gen. Prabowo Subianto, who headed Kopassus, Indonesia's Special Forces, according to the recently leaked official findings of an army investigative panel.

Mr. Patria told the Wall Street Journal that he questions whether Mr. Subianto is qualified to be president because he has never been held fully accountable for his alleged role in human rights violations.

And former army deputy chief Fachrul Razi, who played a key role in Mr. Subianto's honorary discharge from the army, told the Journal that he regrets not pushing for harsher sanctions against Mr. Subianto so that he would not be such a strong candidate now.

Mr. Subianto has said the kidnappings prevented the student activists from staging "bombing and arson" attacks. Of the nine kidnap victims, four support his political party.

Mr. Subianto—who now has a good chance of winning the election July 9 to become Indonesia's next president—was given an honorable discharge from the army after the panel found that he had ordered the nine activists kidnapped.

No criminal charges were filed against Mr. Subianto. In public appearances, Mr. Subianto has indicated he was following orders when his troops carried out the kidnappings, a contention the military panel rejected.

Indonesian presidential candidate Prabowo Subianto, wearing white, high-fives supporters as he campaigns in Banyumas, Central Java province, on Wednesday. Agence France-Presse/Getty Images

Mr. Patria said Kopassus officers seized him at gunpoint, took him to a Kopassus facility and repeatedly beat him. He came close to death when he was given an electric shock that caused agonizing pain and extreme difficulty breathing, he said.

At one point, an interrogator held a gun to his head and told him to pray, he said. After what seemed like 10 minutes, the officer walked away.

"I lost my fear of death," Mr. Patria said. "And what made me sad was only that no one would know if I died."

Mr. Subianto is one of the few who have faced even minimal sanctions for their role in what rights activists say were widespread human rights violations committed during the 32-year reign of Mr. Subianto's autocratic father-in-law, President Suharto. U.S. Ambassador Robert Blake is among those who have called on Indonesia to seek accountability and reconciliation for the abuses of the past.

Those backing Mr. Subianto's main rival in the presidential race, Joko Widodo, have raised the kidnappings as an issue ahead of the election. Earlier this month, Widodo-campaign supporter and former Gen. Wiranto —at one time Mr. Subianto's superior—said Mr. Subianto had ordered the activists' kidnapping on his own initiative and that the action violated army policy. The Subianto campaign says Gen. Wiranto's charge is defamatory.

The unresolved legacy of violence during the Suharto era has left countless victims unaccounted for, including 13 other activists who went missing when Mr. Patria was kidnapped and another who was found dead. In the absence of full accountability, said Mr. Patria, now a journalist, Mr. Subianto's role in human-rights abuses calls into question his suitability for office.

"He is smart," Mr. Patria said. "He has leadership capacity. But the problem is, if he cannot resolve his past and the violation of human rights, I feel he does not deserve to run as president."

Mohammad Mahfud, Mr. Subianto's campaign team manager and a former Constitutional Court chief justice, said in an interview that human-rights violations have occurred for so long and on such a large scale in Indonesia that establishing accountability would be difficult.

The violence dates back to at least 1965, he noted, when an estimated 500,000 suspected communists were slaughtered by soldiers and civilian death squads as then-Gen. Suharto took power. Mr. Mahfud also cited three well-known killings that were carried out by the army to suppress dissent in the 1980s and 1990s.

Some ex-officers who could be held responsible for abuses are supporting Mr. Widodo, he said.

"In the camp of the other presidential ticket, there are a number of military generals who have had problems with human-rights issues," he said. "Why focus on just 1998? Why not go all the way back?"

Prabowo Subianto speaks to supporters during a campaign rally in Jakarta on June 22. Reuters

Anies Baswedan, a spokesman for Mr. Widodo, said the suggested presence of rights violators in the campaign was a "delicate issue" but that the candidate's statements show he is "not going to be soft on this issue."

Mr. Widodo and his running mate, Jusuf Kalla, "have not been implicated with any wrongdoing, so they don't have problems," Mr. Baswedan added. "The other side has problems in that the candidate himself has problems. That's a big difference."

At this point, Mr. Mahfud argues, Indonesia should move on.

"Those political situations in the past should remain just there—in the past," he said.

Mr. Subianto was singled out in 1998 in part because of his ties to President Suharto. But top generals hesitated to deal with him too harshly or in a public forum because of his prominence as the president's son-in-law, said Mr. Razi, one of the seven generals who helped decide his fate.

Mr. Razi said in an interview that he pushed to have Mr. Subianto's case heard by an honorary council of generals rather than have him tried by a military tribunal, thereby keeping military prosecutors from digging into the fate of the other 14 activists. He said he also wanted to prevent harsh treatment of Mr. Subianto, given that he was Mr. Suharto's son-in-law.

"Once it had gone to a military tribunal, it would have been completely out of our control," he said.

The council, made up of Mr. Razi and six other generals, found Mr. Subianto had committed crimes of insubordination and kidnapping. It recommended his discharge but no other sanctions.

The Subianto campaign says the military proceedings were engineered by his military rivals to blacken his name.

Mr. Razi, who backs Mr. Widodo for president, says he regrets letting Mr. Subianto off without further punishment, leaving the door open for his political comeback.

"I am aware that I am the one who is most to blame," he said.

— Yogita Lal and Sara Schonhardt contributed to this article.