Reach Sambath said "the co-investigating judges charged him with crimes against humanity and also with war crimes. The judges have put him in provisional detention" pending further investigation.
Sem Sophal, a police captain, confirmed Nuon Chea had been arrested on charges of crimes against humanity, but did not show a copy of the warrant.
In the 1950s and 60s Nuon Chea helped Pol Pot to seize control of Cambodia's communist movement, later becoming the movement's chief political ideologue during its time in power from 1975-79.
Some two million Cambodians are estimated to have died of hunger, disease, overwork and execution in that time.
Nuon Chea has denied responsibility for the deaths, saying that his only mistake was not paying enough attention to what was happening on the ground, not realising that "bad people" had infiltrated the movement and were killing people.
"I will go to the court and don't care if people believe me or not," he said in July.
Speaking to reporters following Wednesday's arrest, Nuon Chea's son, Nuon Say, said his father was "happy to go shed light on the Khmer Rouge regime for the world and people to understand".
Prosecutors for the UN-backed genocide tribunal investigating crimes by the Khmer Rouge have not yet publicly named Nuon Chea as a suspect.
But he is believed to be one of five surviving senior Khmer Rouge figures they have recommended for trial before the panel.
|Nuon Chea was flown by helicopter to |
Phnom Penh after his arrest [Reuters]
The charges they face include crimes against humanity, genocide, grave breaches of the Geneva Conventions, homicide, torture and religious persecution.
Now in his 80s, Nuon Chea would be the second - and the highest-ranking - Khmer Rouge leader detained to appear before the panel.
However critics of the tribunal say the process has been left too late and suspects such as Nuon Chea may die before ever being brought before a court.
The former head of the notorious S-21 or Tuol Sleng interrogation centre, Kaing Khek Lev, better known as Duch, was charged with crimes against humanity last month.
Duch, 65, unlike Nuon Chea and other former leaders, has been held in a military prison since May 1999.
He is expected to be a key witness in the trial of other leaders.
Ieng Sary, the former Khmer foreign minister; and Khieu Samphan, the former head of state, remain free but are in declining health.
Pol Pot, the leader of the Khmer Rouge, died in 1998. His military chief, Ta Mok, died in 2006.