French HIV-Aids campaign Aides on Thursday notified the media that Moussa, a 28-year-old acrobat who came to France on a temporary work permit in 2015, was taken to Lyon St Exupéry airport on Thursday morning and placed in a cell after refusing to board a plane for Conakry.
His application for asylum was rejected in 2015, despite the fact that homosexuality can be punished by up to three years in jail in Guinea.
He says that before he left the country his partner was murdered by his own family.
His deportation would leader to "almost certain death", according to Aides.
The NGO has called on the official refugees' protection agency, Ofpra, to take up his case.
The organisation says that his not received a request to look into the case but that it is "keen to protest people on account of their sexual orientation, as soon as it is shown that fears about their counrty of origin are justified".
There were demonstrations against the deportation in several French cities on Thursday and Moussa's case has caused a storm on social media.
"His deportation would be a scandal," Socialist Party leader Olivier Faure declared on Thursday.
MPs from President Emmanuel Macron's Republic on the Move (REM) party amended the recently passed immigration law to improve protection for gays.
After contacting the authorities about the case on Thursday, REM MP Laurence Vanceunebrock-Mialon said that Moussa had admitted to lying about his homosexuality to obtain asylum, a claim that gained a vigorous rebuttal from Aides deputy head Christian Andreo.