He was indicted in December 2011 in connection with the disappearances of Sherlyn Cadapan and Karen Empeno, two students at the University of the Philippines who were active in leftist organizations. They were never found, but witnesses later said they had seen the two women in military custody. According to the complaint filed against General Palparan, the women were kept chained in military barracks and were tortured and sexually assaulted by soldiers under the general’s command.

General Palparan, who appeared gaunt and frail when reporters were allowed to question him on Tuesday, denied the allegations. He also said that he stood by his record of aggressively pursuing communist rebels. “I have no regrets for what I’ve done,” he said. “What I did was for the good of the people.”

The Philippines has one of the world’s longest-running communist insurgencies; attacks by the rebels, known as the New People’s Army, take place periodically in both the north and the south of the country. Peace talks broke down in recent months after a series of arrests of high-ranking rebels, although government negotiators say that they continue to seek a deal.

After the dictator Ferdinand E. Marcos declared martial law in the 1970s, members of the Philippine military, police officers and their agents abducted, tortured and sometimes murdered leftist activists with impunity. The practice continued in the years after democracy was restored in 1986, and human rights groups say that it persists today, if to a lesser degree.

President Benigno S. Aquino III, who succeeded Ms. Arroyo in 2010, campaigned for office in part on a promise to address extrajudicial killings, particularly of journalists but also of activists. “President Aquino promised that those who evade the law will be found,” a presidential spokesman, Edwin Lacierda, said Tuesday. “That promise to capture General Palparan has been fulfilled today.”