Fallon was speaking to personnel from 903 Expeditionary Wing at Akrotiri RAF base in Cyprus, from where daily missions are flown against IS.
His visit to the eastern Mediterranean island came just three days after parliament voted to extend Britain's air campaign from Iraq to include Syria.
"We don't go into this lightly," he was quoted in a ministry statement as saying.
"We are very conscious that we are asking our brave armed forces personnel to risk their safety in order to maintain ours."
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Akrotiri has ramped up operations since a US-led coalition began air strikes in September 2014.
Two Tornado fighter bombers joined an existing eight earlier this week and six Typhoon fighters were also flown to the base, the statement said.
"The deployment of Typhoons and two further Tornados will double the number of British fighter jets taking the fight to Daesh.
"Together with extension of our operations to Syria, that will mean we hit these brutal terrorists harder in their heartland.