Peking's Public Security Ministry charged Mr Li with organising illegal gatherings and demonstrations and disturbing public order. It requested the assistance of Interpol over Mr Li and also ordered all police and border control units to be on alert after the demonstrations.
The arrest warrant came after a week of vitriolic attacks on the Falun Gong, in which 1.5 million of the sect's publications were destroyed, and Mr Li was accused of attempting to overthrow the ruling Communist Party.
The 48-year-old founder was born in north-eastern China and claims to have realised that he had supernatural powers, such as mind control and teleportation, from an early age. He set up the Falun Gong which translates as "wheel of law", in 1992 after a career as a trumpet player and grain clerk. Four years later, he published the Zhuan Falun, which is the discipline's bible, and in 1998 moved to Manhattan under what he said was pressure from the Chinese authorities. The United States has already said that it is not planning to co-operate in any extradition request for Mr Li.
Since China outlawed the Falun Gong eight days ago at least 5,000 suspected members of the sect have been arrested. Factories and offices across the country have been forced to identify all former sect members and make them renounce all association with the group.
The campaign, which has taken on overtones of the harsh political attacks of the 1966-1976 Cultural Revolution, has particularly targeted party and army members who were followers of the sect.
The Communist Party's flagship paper the People's Daily said at least seven major provinces and cities would hold rallies to destroy more Falun Gong promotional materialstoday.
Mr Li says the group is apolitical and poses no threat. Believers, who were mainly middle and old-aged city-dwellers, followed a mishmash of Buddhism, Taoism, meditation and breathing exercises.