Foreign Secretary Philip Hammond had announced last week that unmanned Reaper drones were being re-deployed from Afghanistan to the Middle East.
Britain's parliament has authorised air strikes in Iraq, where Tornado fighter jets are part of an international operation conducting bombing raids on IS group targets, but not in Syria.
Fallon also said in a written statement to parliament that the drones would start operations "very shortly".
"Reapers are not authorised to use weapons in Syria; that would require further permission."
During the debate on strikes against targets in Iraq last month, Prime Minister David Cameron said he would return to parliament to seek fresh permission if it was necessary to extend the action to Syria.
But he also stressed that it could go ahead without a parliamentary vote in the event of an urgent humanitarian situation.
The IS group controls large areas of territory in Iraq and Syria, where it has declared an Islamic "caliphate", prompting a US-led coalition to launch air strikes which have so far lasted several months.
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