Nan Yong, who took over as head of the CFA one year ago, was taken away by a police investigative group who were probing a series of matchfixing scandals, Xinhua news agency reported on its website, citing Ministry of Public Security officials.
CFA vice president Yang Yimin and Zhang Jianqiang, who was formerly in charge of referee arrangements, were also taken in by police, the newspaper added.
Zhang now oversees women's football at the CFA.
The three were questioned by police to "clarify some facts in several important cases of soccer gambling and illegal manipulating domestic soccer league games by using business bribery," the Xinhua report said.
Jia Xiuquan, former head coach of Chinese Super League (CSL) club Shanghai Shenhua, was also questioned by police, the Beijing Times said on Thursday.
The CFA has cancelled at least two meetings which were to be attended by Nan and Yang, while arranging other officials to take charge of their jobs, the Soccer News said.
Nobody at the CFA was immediately available to comment.
At least 21 officials, players and club managers, including Xu Hongtao, the president of Chengdu Blades, owned by England's Sheffield United, have been arrested or detained in the past two month on suspicion of matchfixing or gambling, which is illegal in China.
A local court sentenced former Liaoning player Lu Dong to jail for three years for gambling, the Beijing News said on Thursday. Lu Dong was not involved in matchfixing.
The probe into matchfixing followed a string of comments in recent months by top Communist Party officials on the need to clean up the men's professional game in China, which is widely perceived as being riven with corruption.
