BBC has reported that the flight was stopped after a late intervention from the European Court of Human Rights (ECtHR) led to fresh challenges in the UK courts.
The cancellation of the flight followed days of arguments in UK courts, ending with the home secretary getting the go-ahead to begin transporting some of the asylum seekers.
After the judgement from the ECtHR, passengers were removed from the plane which had to take off on Tuesday at 11:30 p.m. of Kigali Time.
BBC has reported that the Boeing 767, chartered at an estimated cost of £500,000, had been due to take off from a military airport in Wiltshire.
UK Home Secretary Priti Patel said she was "disappointed" but added that preparation for the next flight continues.
“I have always said this policy will not be easy to deliver and am disappointed that legal challenge and last-minute claims have meant today’s flight was unable to depart,” she said.
“We will not be deterred from doing the right thing and delivering our plans to control our nation’s borders. Our legal teams are reviewing every decision made on this flight and preparations for the next flight begins now,” added Patel.
The human rights court said that one migrant from Iraq onboard the plane was not supposed to be deported.
It also maintained that UK must wait for the final courts’ judgement next month before further action.