The order comes a day after the strongman premier threatened the Cambodia Daily, one of the country's few remaining critical newspapers, with closer over an alleged unpaid tax bill of $6.3 million, calling them "thieves".
In a statement on Wednesday the Ministry of Foreign Affairs said foreign employees of the National Democratic Institute (NDI) have seven days to leave after the group allegedly failed to formally register or pay correct taxes.
"Authorities are geared up to take the same measures against any foreign association or non-government organisation that fails to abide" by Cambodia's laws, the statement added.
In recent weeks a string of foreign-funded organisations including the NDI have been named in Cambodia's pro-government press or by officials as facing tax or regulatory probes.
Analysts say the cascade of legal cases is straight from the political playbook of Hun Sen, who has cornered opponents throughout his three-decade rule, in the run-up to elections.
Cambodians are due to go to the polls in just under a year, in a poll many expect to be a close-run affair.
Apart from the Cambodia Daily, which is owned by an American, the US-funded Radio Free Asia and Voice of America have also been legally targeted.
All have denied wrongdoing and said they are being selected for their independent reporting.
In a statement, the Overseas Press Club of Cambodia said the Cambodia Daily "has a history of running stories that have angered the government, leading many to believe the tax department is being used to target critics" before the poll.
The NDI, which says it works to strengthen democratic institutions worldwide, has been operating in Cambodia since 1992.
A country ravaged by war
In recent weeks, pro-government media have accused the organisation of helping Cambodia's opposition party to try to topple the government.
The NDI, chaired by former US Secretary of State Madeleine Albright, did not immediately respond to requests for comment.
But they have previously declared themselves as "strictly non-partisan", adding they also trained many members of Hun Sen's ruling party.
To supporters, Hun Sen - one of the world's longest serving leaders - has brought growth and stability to an impoverished country ravaged by decades of war.
But critics say corruption, inequality and rights abuses have also flourished.
Growing closer to China
In recent years he has grown closer to China while criticising the US, one of Cambodia's largest donors.
In 2015 the government passed a broadly-worded law regulating NGOs. Critics warned the legislation would make it much easier to shutter organisations deemed critical of the government.
Impoverished Cambodia is home to some 5,000 NGOs.