China was in the process of verifying details with Malaysia and hoped that the Southeast Asian nation would "attach great importance" to its concerns, China's Foreign Ministry said in a faxed statement to Reuters.
"These people are all Chinese nationals. We resolutely oppose them being deported to a third country," it said.
Prosecutors in Muslim-majority Malaysia dropped charges against the Uighurs on humanitarian grounds and they arrived in Turkey after flying out of Kuala Lumpur on Tuesday, their lawyer, Fahmi Moin, said on Thursday.
The Malaysian government has yet to comment on the matter.
The Uighurs in Malaysia were part of a group of more than 200 detained in Thailand in 2014.
Although they identified themselves as Turkish citizens and asked to be sent to Turkey, more than 100 were forcibly returned to China in July 2015, sparking international condemnation.
The Uighurs were detained and charged with illegally entering Malaysia after breaking out of the Thai prison last November by punching holes in a prison wall and using blankets as ladders.
Malaysia's move is likely to strain ties with China, already tested since Mahathir Mohamad became prime minister after a stunning election victory in May and cancelled more than $20 billion worth of projects awarded to Chinese companies.
In February, Reuters reported that Malaysia was under great pressure from China to deport the men there, citing sources. Some Western missions sought to dissuade it from sending them to China, which has been accused of persecuting Uighurs.
Beijing accuses separatist extremists among the Uighur minority of plotting attacks on China's Han majority in the restive far western region of Xinjiang and elsewhere.
China has been accused of rights abuses in Xinjiang, torture of Uighur detainees and tight controls on their religion and culture. It denies wrongdoing.
In February, Malaysia said it was considering China's request to extradite the 11 men. In the past, it has sent some detained Uighurs to China.
Their detention came as Malaysia drew closer to China under former prime minister Najib Razak, but 93-year-old Mahathir, in his second stint as premier, has been vocal in backing Muslim communities against persecution.
In its statement on Friday, China's Foreign Ministry said it was against illegal immigration in any form.
(With inputs from agencies.)