Home Secretary R.K. Singh told reporters that Mohammed Afzal Guru was executed early Saturday morning at New Delhi's Tihar prison.
"It was the law taking its course," Singh said.
Guru was given a Muslim burial in the prison compound, Press Trust of India news agency reported. His family in the India's Jammu-Kashmir state has demanded that his body be handed over, but that seems unlikely given the highly sensitive nature of the execution.
Guru had been on death row since first being convicted in 2002. Subsequent appeals in higher courts were also rejected, and India's Supreme Court set an execution date for October 2006. But his execution was delayed after his wife filed a mercy petition with India's president. That petition, the last step in the judicial process, was turned down earlier this week.
Several rights groups across India and political groups in Indian Kashmir have said that Guru did not get a fair trial.
"Serious questions have been raised about the fairness of Afzal Guru's trial," Shashikumar Velath, Amnesty International India's programs director, said in a statement. "He did not receive legal representation of his choice or a lawyer with adequate experience at the trial stage. These concerns were not addressed.
Protests broke out Saturday in at least four parts of Indian Kashmir, including the northwestern town of Sopore, which was Guru's home. Scores of protesters chanting slogans including "We want freedom" and "Down with India" defied a curfew and clashed with police and paramilitary troops, who opened fire. Four protesters sustained bullet wounds and one of them was in critical condition, a senior police officer said on customary condition of anonymity.
Thousands of police and paramilitary troops fanned out across the state preparing for more protests and violence following the announcement of the execution. A curfew was also imposed in most parts of Indian Kashmir, and cable television channels were cut off in the region.
About 30 Kashmiri students and anti-death penalty activists clashed with Indian police and right-wing Hindu groups in New Delhi. Most of the protesters were detained by the police.
Police in Indian Kashmir on Saturday also detained several leaders of the All Parties Hurriyat Conference, an umbrella organization of separatist political and religious groups, a police officer said on condition of anonymity because he wasn't authorized to speak to reporters.
The group called for four days mourning in the disputed region and called Guru's hanging "an attack on the collective conscience of the Kashmiri people."
"We appeal to the people to rise in one voice and protest this aggressive act so that it's known to everyone that even if the heads of Kashmiris are cut, they'll never bow under any circumstances," the group said in a statement.
The statement said that Indian Kashmir's chief cleric, Mirwaiz Umar Farooq, who also heads the separatist alliance, was detained in New Delhi and not allowed to travel to Srinagar, the main city of Indian Kashmir. Another top separatist leader, Syed Ali Geelani, was also detained in the Indian capital, according to news reports.
When Guru's death sentence was handed down by India's Supreme Court it sparked protests in Kashmir, and the state government has warned that his execution could destabilize the volatile Himalayan region.
Anti-India sentiment runs deep in Muslim-majority Kashmir, which is divided between Hindu-dominated India and Muslim-majority Pakistan but is claimed by both nations.
There were a few small protests against the execution in different parts of Pakistan on Saturday, none larger than about 100 people. Jamaat-ud-Dawa, believed to be a front for the anti-India militant group Lashkar-e-Taiba, organized a rally of about 100 people in the southern port city of Karachi and another roughly half that size in the capital, Islamabad. About 100 people protested in the main city of Pakistan-held Kashmir, Muzaffarabad. The protesters held banners and chanted slogans condemning India.
Since 1989, an armed uprising in Indian-controlled Kashmir and an ensuing crackdown have killed an estimated 68,000 people, mostly civilians.
The secrecy in which Guru's execution was carried out was similar to the execution in November of Mohammed Ajmal Kasab, the lone surviving gunman of the 2008 Mumbai attacks. Kasab was also buried in the western Indian prison where he was hanged.
On Dec. 13, 2001, five gunmen entered the compound of India's Parliament and opened fire. A gunbattle with security officers ensued and 14 people, including the gunmen, were killed. India blamed the Pakistan-based militant groups Lashkar-e-Taiba and Jaish-e-Mohammed.
The attack led to heightened tensions between India and its neighbor and archrival Pakistan and brought the neighbors to the brink of war, but tensions eased after intense diplomatic pressure from the international community and a promise by then-Pakistani President Gen. Pervez Musharraf to clamp down on the militants.
Guru confessed in TV interviews that he helped plot the attack, but later denied any involvement and said he was tortured into confessing.
Government prosecutors said that Guru was a member of Jaish-e-Mohammed, a charge Guru denied.
Guru's family said it had not been told that he was about to be executed.
"Indian government has yet again functioned like a fascist state and hanged him secretly," said Yasin Guru, a relative who lives in the family's compound in Sopore. "They did not have the courtesy to inform his family."
Associated Press writers Aijaz Hussain in Srinagar, India, and Adil Jawad in Karachi, Pakistan, contributed to this report.