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The Boeing 767 - operated by Spanish charter firm Privilege Style - was seen landing at the Ministry of Defence testing site in Wiltshire earlier today.
Judges decided that the plane to the African country could take off as official figures showed 138 people made the perilous journey across the English Channel in three boats.
One of the seven migrants due to be transferred to Rwanda had his removal called off after a move by the European Court of Human Rights, while a second man's move is also thrown into doubt.
The arrivals on Sunday were first to make the crossing in five days, and included a number of women and small children. This was followed by another 35 migrants who made the crossing today.
The number of would-be refugees arriving by dinghy is more than double the figure for this time last year, official figures show.