It is home to Army Air Corps Apache helicopters that have been involved in recent conflicts including Afghanistan.
A Ministry of Defence spokesman said an inquiry was taking place. Action would be taken against those who fell short of the Army's high standards, he said.
"As there is an on-going investigation into this allegation it would be inappropriate to comment further," he added.
Wattisham air station is home to 3 and 4 Regiment Army Air Corps.
Prince Harry, who qualified as an Apache helicopter pilot, is stationed at the base.
The Ministry of Defence spokesman would not confirm if he was there at the time of the alleged attack.