A total of 2,318 people were arrested or indicted on charges of "endangering state security", the US-based Dui Hua Foundation said, citing statistics from China's central prosecution office.
The offence of "endangering state security" replaced that of "counter-revolution" in the 1990s, and is primarily aimed at suppressing political dissent, but also applies to espionage.
In recent years it has been applied to members of Tibetan and Uighur minority ethnic groups who have demanded greater civil rights or spoken out against alleged government abuses.
The majority of those whose cases were known to Dui Hua in 2013 appeared from their names to be Tibetan or Uighur, despite such groups making up a small minority of China's population.
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Since Xi Jinping became China's president in 2013 the Communist party has launched one of its toughest crackdowns on political critics in decades.
The number of arrests and prosecutions for endangering state security was around three times that of a decade ago, when Xi's predecessor Hu Jintao took power, Dui Hua said.
China has also cracked down on fringe religious groups under Xi, with official statistics showing 1,554 trials in 2013 for membership or leadership of "illegal cults", a 60 percent rise year on year, Dui Hua said.
Figures for 2014 have not been released, but the year saw several high profile state security cases, including Uighur academic Ilham Tohti, who was convicted of separatism and sentenced to life in prison.
His conviction drew outrage from rights groups, who said he had been punished for his persistent moderate criticism of China's policies in the mainly Muslim far-west Uighur homeland of Xinjiang.