Legal threats forced Kem Sokha's predecessor, Sam Rainsy, to resign this year from the Cambodia National Rescue Party he once led.
Speaking to 4,000 Cambodian garment factory workers Sunday, Hun Sen claimed Kem Sokha had colluded with the United States against his government and warned the opposition party it could be dissolved if it defended him.
"We have been a burr in Hun Sen's side for the entire time that we have been operating", said The Cambodia Daily's American editor-in-chief, Jodie DeJonge.
CNRP gained strength as the opposition party to the ruling Cambodian People's Party in national elections in July 2013 and in municipal elections in June this year.
Mr. Kem Sokha's arrest was quickly condemned by opposition leaders and worldwide human rights activists.More news: Angry movie for angry times: George Clooney defines latest directorial 'Suburbicon'
If Kem Sokha is found guilty of any offence, it could allow the government to shut the party under a new law that forbids parties from having a leader who has been convicted.
Kem Monovitthya, one of the politician's daughters, said on Facebook that her father had been handcuffed and taken away after hundreds of policemen raided his home.
During the speech he boasted that the U.S. was "advising me about strategies to change the dictatorship in Cambodia".
One of Cambodia's most stridently independent newspapers, The Cambodia Daily, published its last edition on Monday with the headline "Descent Into Outright Dictatorship" as it closed amid a crackdown on critics of Prime Minister Hun Sen.
He portrays himself as the only person who can bring stability and prosperity to a country once ravaged by civil war and genocide.More news: County cricket match abandoned as 'crossbow bolt' lands on field
But there is rising anger, especially among the youth, over how that wealth is spread and the cronyism that remains endemic under his rule.
Mr Hun Sen added that the national elections would proceed as usual. In August, at least 15 radio stations broadcasting content from Radio Free Asia, Voice of America, Voice of Democracy, and other foreign networks were shut down by the government for "violation of contracts" with the information ministry.
Among the media in the firing line is the well respected Cambodia Daily, which often criticises the government.
The government last month billed The Daily for $6.4 million in taxes and was later told to pay the bill or "pack up and go".
The publication was founded in 1993 by an American journalist, making it a particular target for Hun Sen, who has accused the United States of plotting with the opposition against his government.More news: North Korea: Theresa May urges China to intervene
It says the hefty bill was invented by the government and not based on an audit of its books.
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