Independent travel to Taiwan will be suspended from Thursday, given current cross-Straits relations, according to a Ministry of Culture and Tourism statement on Wednesday.
The so-called self-guided travel to Taiwan has been trialled since June 2011.
Under the terms of the program, mainland residents in 47 cities including Beijing, Shanghai and Xiamen in Fujian province can apply for individual entry permits to Taiwan.
Travel agency sources said that all tourists with plans to visit Taiwan now have to join tour groups.
China has increased pressure on Taiwan, putting the onus on the administration of President Tsai Ing-wen who is seen as pro-independence.