We　propose　two　deterministic　schemes　to　implement　quantum　swap　gate　and　Fredkin　gate　encoded　by　atomic　qubits　through　the　input-output　process　of　the　cavity.　We　show　that　these　schemes　can　be　extended　to　realize　multi-qubit　gate　operations.　By　numerical　calculation,　the　fidelity　and　photon　loss　probability　for　implementing　quantum　swap　gate　between　photon　and　atom　are　also　discussed.　©　2009　Europhysics　Letters　Association.