Thousands of asylum seekers are missing (Image: Getty)
Just 700 of 5,000 people identified for deportation are still in "regular contact" with the Home Office, according to official documents.
Home Office insiders reportedly admitted the department has "limited capability" to locate migrants once they have left state-funded accommodation.
An official risk register says the top challenge is that Home Office officials do not locate or detain enough migrants or face legal challenges when trying to launch deportation flights to Rwanda, which would leave them without anyone to send.
It also lays out potential problems transferring migrants from removal centres to the airfield, with protests, bad weather conditions or commercial contractors refusing to do the work all listed.
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Military planes are being considered as a potential back up plan. However, the military is reportedly resisting the move, the Telegraph reported.
Read more All the questions on the Rwanda Bill answered
The documents also outline the potential for Rwanda not being ready to take on new arrivals if the scheme gets under way, which would lead to migrants being returned to the UK.
The Government has “worked extensively” with Rwanda in recent month to increase its capacity to process asylum seekers.
Home Office experts have helped to train their Rwandan counterparts, judges and lawyers in the east African nation.
A new treaty signed last year to address concerns raised by the Supreme Court about sending migrants to Kigali includes provisions to stop anyone deported being sent on to any other country other than the UK.
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Yvette Cooper, shadow Home Secretary, said: “This is more evidence of Tory chaos on asylum and immigration. Their extortionate and failing Rwanda plan is already costing the taxpayer up to ￡400million without a single person being sent, and now we learn that thousands who were due to go have ‘gone missing’.
‘‘This is presumably on top of the 17,000 people the Home Office’s Permanent Secretary acknowledged had disappeared from backlog. It’s time the Prime Minister and Home Secretary got a grip on the mess they have created.
“Instead of wasting even more time and money on the Rwanda scheme that no one believes will work, the Conservatives should adopt Labour’s plan of going after the criminal smuggling gangs making millions from small-boat crossings and speeding up removals by recruiting 1,000 additional staff to form a new fast-track returns unit."
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