The deal, which has been deemed “unworkable” by the UN refugee agency, was signed off by the Home Secretary using a ministerial direction due to concerns raised by civil servants .
A ministerial directive has rarely been used and means Ms Patel must take personal responsibility for the policy.
However, union bosses have labelled the immigration deal as “divisive” and said some civil servants may leave in protest against the policy which will see those who cross the Channel illegally, sent to the east Africa state.
“Civil servants know their job is to support the government of the day,” said Dave Penman, general secretary of the FDA (Association of First Division Civil Servants). “They sign up for that knowing they might not like what the government does.
"On the more divisive policies, which this clearly is, they face a choice - implement or leave. That could mean elsewhere in the Home Office, another department, or the service."
The Government has agreed to pay £120million to Rwanda in order to take on people who have been deemed to entered the UK unlawfully since January 1. A set cost of between £20,000-30,000 will be allocated to each individual for their flight and for the first three months of their stay in the country.
Mark Serwotka, general secretary of the Public and Commercial Services (PCS) Union said the policy was “inhumane”.
He added: “We have already seen that they are prepared to risk lives by turning boats back in the channel - a policy which we have had to take them to court over. It is a heartless approach that displays total disregard for human life which everyone must oppose.’’
According to the Home Office, over 6,000 people have crossed the Channel since the start of the year, while 28,526 crossed the year before.