Three Muslim men two Thais and an Egyptian were charged Wednesday with international terrorism and links with Jemaah Islamiyah, the Islamic extremist group, officials said.
Authorities also ordered the expulsion within 72 hours of 28 foreigners who had been teaching at an Islamic school.
"This operation has foiled any attempts of terrorist activity" in Cambodia, said Om Yentieng, a senior adviser to Prime Minister Hun Sen.
Oun Bunna, an investigating judge at the Phnom Penh Municipal Court, said the three suspects were charged with "international terrorism with links to JI." If convicted they face 20 years to life in jail.
Jemaah Islamiyah, or JI, is linked to Osama bin Laden's al-Qaida terror group and wants to set up an Islamic state in Southeast Asia. Its alleged operations chief has confessed to helping plan the Bali bombings last year that killed 202 people, and the group allegedly planned a series of foiled attacks on Western interests in the region.
The three suspects, who were arrested Sunday, were identified as Abdul Azi Haji Thiming and Muhammad Jalaludin Mading of Thailand, and Esam Mohammed Khidr Ali of Egypt.
The police are conducting further investigations, Oun Bunna told reporters after questioning the suspects, adding that it could take up to six months before the three suspects come to trial.
Oun Bunna and other officials refused to disclose details about the arrests and the suspects' activities.
"I'm not saying anything in English," Ali told reporters in response to questions on why he was arrested, as he was led from the courtroom.
Om Yentieng said police have established that the suspects had links "with terrorism activities overseas." He did not elaborate.
He said they are believed to be linked to a Cambodian Muslim organization called Om Al Qura, which has operated a religious school near the Cambodian capital of Phnom Penh for the past five or six years.
Twenty-eight foreigners who had been teaching at the school were ordered Wednesday to leave the country within 72 hours. The teachers targeted for expulsion are from Nigeria, Pakistan, Sudan, Thailand, Yemen and Egypt, Om Yentieng said.
Police officers involved in keeping a watch on Om Al Qura's activities said the three suspects were arrested while walking along a main road near their organization, which is located about 25 kilometers (15 miles) north of the capital, Phnom Penh.
Most Cambodian Muslims belong to the Cham ethnic minority, who make up less than 5 percent of the country's 12.5 million people in this mostly Buddhist country.
The government had said in the past that local Muslims have no active links to militant groups.
But intelligence sources said last November that a handful of suspected al-Qaida agents traveling on false passports had entered Cambodia in 2001 and 2002, sometimes staying for several weeks as guests of local Muslims.
Although Cambodia had not been directly linked with al-Qaida or the JI, security analysts have expressed concern that the country's weak border controls and poor law enforcement could make it a haven for militants seeking a hiding place.