Pol Pot's 'Brother No 2' is charged with crimes against humanity

The most senior surviving member of the Khmer Rouge regime, Nuon Chea, was arrested yesterday at his home in the Cambodian jungle and flown by helicopter to the capital, Phnom Penh, where he was charged with war crimes and crimes against humanity.

Nuon Chea, nicknamed Brother Number Two, served as the right-hand man to the Khmer Rouge's leader, Pol Pot. He is the second person to be brought before a UN-backed genocide tribunal. In July, Kaing Guek Eav, known as Comrade Duch, was charged by the tribunal, which is finally starting work after years of negotiations between Cambodia and the UN.

Chea, who had been living freely since striking a deal with the government in 1998, was arrested at dawn after Cambodian special forces soldiers and Western security guards surrounded his small wooden house in Pailin, near the Thai border. He was questioned by court officials, and then flown off by military helicopter. Photographs, correspondence and documents – said by his son, Nuon Say, to be material that Chea had written about the Khmer Rouge – were also seized. A convoy of nearly a dozen vehicles transported him to the helicopter.

The 82-year-old was imprisoned in the tribunal compound after a short hearing before the court, made up of Cambodian and international judges. He is the most senior commander to be brought to account over the atrocities of the Khmer Rouge regime, which oversaw the deaths of an estimated 1.7 million people between 1975 and 1979.

After reaching his deal with the government, which included former Khmer Rouge members, Chea made a bizarre apology to Cambodians, saying: "Naturally we are sorry – not only for the lives of the people, but also for the animals. They all died because we wanted to win the war."

For years it seemed as if men like him would never be brought to trial. The UN first recommended a genocide tribunal in 1999. But it took until last year for the tribunal to be established and until this year for it to start work. Those seeking justice feared that more of the Khmer Rouge's elderly former leaders would die in the meantime.

The $56m (£28m) tribunal, based in the western outskirts of Phnom Penh, has begun proceedings against three other men. It has not named them, but they are believed to be the former president, Khieu Samphan, the former foreign minister, Ieng Sary, and Meas Muth, the son-in-law of Ta Mok, Pol Pot's former military chief, who died last year. Like Chea, those men have been living freely – Khieu Samphan in Pailin, next-door to "Brother Number Two".

After declaring their "Year Zero" revolution in 1975, the black-shirted Khmer Rouge emptied the cities, exiling millions of people to vast collective farms. The Chinese-backed regime abolished religion, money and schools, and tried to eradicate the intelligentsia, in an effort to transform Cambodia into an agrarian, peasant utopia. Many people were executed – some at the "Killing Fields" on the outskirts of Phnom Penh, after being imprisoned in the Tuol Sleng interrogation centre. Others died of starvation, disease or overwork. Kaing Guek Eav headed the notorious prison, and Chea allegedly sent thousands of people to the centre, ordering guards to execute individuals and groups.

The regime was toppled by invading Vietnamese troops in 1979, but the Khmer Rouge fought on in pockets. In 1998, Pol Pot died in their last remaining stronghold of Anlong Veng. Later that year, the remnants of his ultra-Maoist guerrilla army, including Chea, surrendered.

Chea, who trained as a lawyer in Thailand, joined the Khmer Rouge in the 1950s, when it was evolving into an underground Communist party. He later became its chief political ideologue, and was allegedly a key architect of its genocide policies. In an interview with Agence France Presse earlier this year, he claimed: "I was not involved in the killing of people. I don't know who was responsible."

His son said yesterday that his mother had fainted when her husband was taken away. He said his father rolled down the car window to take a last look at him, but said nothing.

Dozens of villagers gathered to watch the arrest. "[Chea] was shaking. He looked like his legs would collapse," a neighbour, Sok Sothera.

Chhum Manh, one of the few people who survived incarceration in Tuol Sleng, said: "I'm happy that they have brought him for questioning. I was afraid he would die like Tai Mok. But Nuon Chea is not enough." He said he was not after revenge. "We want them to apologise to the people so that we can be at peace," he said.

The tribunal's first trial is to be held next year.