Isa Muaza, who has refused almost all food for more than three months and is said to be near death, was flown out of the UK on Friday after a last-ditch legal challenge failed.
But he had to be brought back via Malta when Nigerian authorities apparently refused the chartered plane permission to land.
The 47-year-old, from Maiduguri in the northeast of Nigeria, entered the UK in 2007 on a visitor's visa but did not leave when it expired.
After being detained for removal as an overstayer, he claimed asylum on the grounds that members of hardline Islamist group Boko Haram wanted to kill him.
The claim was rejected as "manifestly unfounded" in August, prompting his hunger strike.