The group, ChinaAid, also says high-level talks are under way between US and Chinese officials over his fate.
Earlier, fellow activist Hu Jia said Mr Chen was in the US embassy. Neither country has commented on the claims.
Mr Chen's escape could overshadow a visit to Beijing next week by US Secretary of State Hillary Clinton.
She has repeatedly called for the dissident's release.
A statement from the Texas-based ChinaAid group said it had "learned from a source close to the Chen Guangcheng situation that Chen is under US protection" in Beijing.
The group is led by Bob Fu, an American-based human rights campaigner and friend of Mr Chen.
On Friday, Hu Jia - another friend of Mr Chen and himself a prominent activist and dissident - told the BBC he had met Mr Chen in the US embassy in Beijiing in the last 72 hours, after his escape from house arrest in the eastern province of Shandong. He said Mr Chen had scaled a high wall before being driven hundreds of kilometres to Beijing.
On Saturday, Mr Hu's wife Zeng Jinyan said on twitter that he had been taken away for questioning by local police.
Watch from Reuters: