Issa Qarage, minister of detainees, told WAFA news agency that Israel was already making preparations for Allan's return to the West Bank.
Allan, a Palestinian lawyer, has been imprisoned by Israel without charge since November 2014.
The activist went on hunger strike in June 2015, to protest at his illegal detention. Allan went into a coma two months later, and 18 August he slowed regained consciousness after Israel agreed to review his case.
On 20 August, the Israeli Supreme Court suspended his detention order, partly due to his failing health. Israel feared his death could spark new uprisings in the Occupied Territories.
Human rights groups and Palestinian activists believe the decision to be unjust.