Reach Sambath, a tribunal spokesman, said: "The co-investigating judges have detained him for a period of one year."
"Khieu Samphan's lawyers have already said they will appeal his detention."
He also said that Jacques Verges, a French lawyer, will defend the 76-year-old former head of state.
Khieu Samphan was previously arrested days after he was admitted to a hospital in Phnom Penh, the Cambodian capital.
He was reportedly being treated for a stroke.
War crimes charges Khieu Samphan's detention had been expected, following the arrest last week of Ieng Sary, the Khmer Rouge's ex-foreign minister, and his wife Ieng Thirith, the government's social affairs minister.
They were both charged with crimes against humanity, while Ieng Sary was also charged with war crimes.
The first trials under the tribunal are expected to begin next year.
Up to two million Cambodians are thought to have died through starvation, overwork or execution during the government's 1975-79 rule.
But senior members of the Khmer Rouge have not faced trial.
Contested history Khieu Samphan denied the government's policies in a new book published days before his arrest.
Reflection on Cambodian History from Ancient Times to the Era of Democratic Kampuchea defends the government and labels Pol Pot, its leader, as a patriot.
While acknowledging that people had died, Khieu Samphan said deliberate mass killings never took place.
"There was no policy of starving the people. There was no policy of mass killings," he wrote.
"The regime always thought about the people's well-being."
Researchers admit that there is not as much evidence against Khieu Samphan as against other leaders, but they say that he was aware of the Khmer Rouge's execution policies and did nothing to stop them.
However, Verges, his lawyer, famous for defending Klaus Barbie, a Nazi war criminal and Ramirez Sánchez, a former left-wing fighter, known as "Carlos the Jackal", claims that his client was not one of the government's policymakers.
"The Khmer Rouge leadership did not resort to persuasion but to coercion, and, eventually, crimes against human beings. Khieu Samphan never took a direct part in these crimes," Verges said in the preface to Khieu Samphan's memoirs, published in 2004.