Mr Allan was taken back into detention on his release from hospital.
He had suffered brain damage after spending 65 days without food.
Mr Allan, an alleged member of the militant group Islamic Jihad, began refusing food in protest at being held indefinitely under a controversial policy of administrative detention.
The detention order had been suspended by a court ruling while he was in hospital, because of his medical condition.
Relatives say he plans to resume his hunger strike now that he has been returned to detention.
The administrative detention system allows a military court to order suspects to be detained indefinitely, subject to renewal every six months by a court, without charge or trial.
Israel previously offered to release Mr Allan when his current six-month period of administrative detention expired on 3 November, if he agreed to end his hunger strike.
Mr Allan's protest has continued despite Israel's parliament passing a law in July that would allow the authorities to force-feed detainees to keep them alive.
The Israeli justice ministry has alleged that Mr Allan is involved in "grave terrorism". It says "classified information" warrants keeping him detained.
Mr Allan denies the allegations and any involvement with Islamic Jihad.
The Israeli authorities have re-arrested Mohammed Allan, who had staged a hunger strike to protest against his detention without charge.