Wing Commander Jonathon Moreton spoke warmly of Squadron Leader Samuel Bailey who is missing presumed dead.
He also paid tribute to Flight Lieutenant Adam Sanders who is still missing after Tuesday's crash.
The RAF has paid tribute to a Tornado pilot killed in a crash off the coast of Scotland earlier this week.
Wing Commander Jonathon Moreton described Flight Lieutenant Hywel Poole as a "capable and confident pilot" with an "infectious personality".
Two Tornado crewmen are still missing but are presumed to have died in Tuesday's crash.
The sole survivor of the accident remains in a serious but stable condition in hospital.
Defence Secretary Philip Hammond has paid tribute to three Tornado jet crew lost in a crash in the Moray Firth earlier this week.
He told MPs: "My thoughts - and, I am sure, those of the entire House - are with their loved ones at this difficult time, and with the fourth member of the squadron involved in the incident, who is currently in a serious but stable condition in hospital."