The Foreign Office would not say how Mr Johnson got to Brussels after the emergency landing, saying it does not comment on travel plans.
A spokesman for Luton Airport said: "At 5.26pm an RAF aircraft landed safely at London Luton Airport after reporting a technical issue.
"Emergency procedures were put in place and all 16 passengers left the aircraft safely. Several scheduled flights were disrupted whilst the runway was cleared. The runway reopened at 17.59."