Yusef Abbas, Saidullah Khalik, and Hajiakbar Abdul Ghuper are the last of 22 Muslim minority Chinese nationals to be moved from the Guantanamo Bay military prison in Cuba, according to the Pentagon.
Slovakia's Interior Ministry confirmed that it would take in the three. Uighurs are a Turkic-speaking Muslim people from China's far western region of Xinjiang.
Chinese Foreign Ministry spokesperson Qin Gang said the three were members of the separatist East Turkestan Islamic Movement, which Beijing labels a terrorist group.
"They are genuine terrorists. They not only threaten China's security, they will threaten the security of the country that receives them," he told a daily news briefing. "China hopes that the relevant country ... does not give asylum to terrorists, and sends them back to China as soon as possible."
Qin added that China did not appreciate a recent US State Department call for Chinese security forces to exercise restraint following the latest outbreak of violence in Xinjiang, also blamed by Beijing on "terrorists".
"These remarks neglect the facts and are feeble," he said.
"We urge the United States to abandon their double standards when it comes to terrorism, and immediately stop saying one thing and doing another, to avoid sending the wrong message to violent terrorist forces."
The United States said it was grateful to Slovakia for its "humanitarian gesture."
Most of the Uighurs at Guantanamo were captured near the Pakistan-Afghanistan border in late 2001, and were believed to have trained with the Taliban. US officials have deemed they pose no threat to the United States.
In 2008, a US court had ordered that they be released.
They have been resettled in El Salvador, Switzerland, Bermuda, Albania, and the Pacific island nation of Palau. The US government has said it will not return the Uighurs to China because they would face persecution there.
"We've long maintained our position that we will not repatriate Uighurs to China from Guantanamo due to our humane treatment policies," US State Department spokesperson Marie Harf said at a briefing in Washington on Thursday.
"We remain deeply concerned about discrimination and restrictions placed on Uighurs and other Muslims in China," she said.
Many Uighurs chafe at restrictions on their culture, language and religion, though the Chinese government insists it grants them broad freedoms. The region has been beset by violence with at least 91 people, including several police, killed in unrest in Xinjiang since April, according to state media reports.
China has blamed some of the violence on militants with connections to foreign groups, including al Qaeda, plotting holy war. Many rights groups and exiles say China exaggerates the militant threat to justify its firm grip on energy-rich Xinjiang, which abuts Central Asia, Afghanistan, Pakistan and India.
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It's obvious that the USA cares more about Muslim persecution in China than Pakistan - that must be a bitter pill to swallow.