Eritrea, Ethiopia and Turkey also figured prominently on the list.
The report released early today says a quarter of the 199 journalists worldwide who were in prison as of December 1 because of their work were in China.
The Communist Party-run country under President Xi Jinping had 49 journalists behind bars, the highest number for China since the CPJ began its annual survey in 1990.
The report also singled out three jailed Chinese who were not included on its annual list: the three brothers of a US-based journalist with Radio Free Asia who covers China's treatment of his ethnic group, the Muslim Uighurs.
Egypt was second on the list with 23 journalists in prison, up from a dozen a year ago and zero in 2012.
"Perhaps nowhere has the climate for the press deteriorated more rapidly than in Egypt," the report says, accusing President Abdel-Fattah el-Sissi of acting under the pretext of national security since he took office in 2014 a year after the military ousted Islamist President Mohammed Morsi.
In August, el-Sissi approved a law that included heavy fines for journalists who don't follow the government line. Washington Post reporter Jason Rezaian is among the 19 journalists that the CPJ lists as being behind bars in Iran, an Islamic republic under Supreme Leader Ayatollah Ali Khamenei and President Hassan Rouhani.
The report expresses special concern about Turkey, where the number of jailed journalists doubled over the past year to 14.
Late last month, hundreds of protesters chanted "Free press cannot be silenced" after journalists Can Dundar and Erdem Gul were jailed on terror and espionage charges for their reports on alleged Turkish arms smuggling to Syria.
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