Whilst preparing for deployment to Exercise Crocodile 99, 2AFDS, along with No. 381 Expeditionary Combat Support Squadron (381ECSS) and 382ECSS, were warned out for duty in East Timor on Operation Warden. Both 381ECSS and 382ECSS had ADGs and GRDEFOs on strength. 2AFDS and 381ECSS commenced deployment to Comoro Airfield, Dili, on 20 September 1999; 381ECSS began arriving at Cakung Airfield, Baucau on 11 October 1999. 2AFDS undertook static security, access control and reconnaissance patrol tasks, in addition to establishing observation posts and providing a Quick Reaction Force (QRF). Reinforcements arrived on 4 November 1999 comprising 37 members of 3AFDS, an integrated permanent and reserve squadron headquartered at RAAF Base Amberley (subsequently disbanded in December 2006). The additional manpower also allowed the squadron to assume responsibility for the Dili heliport in December.