Unmanned aerial systems (UASs) create an extensive fighting capability of the developed military forces. Particularly, these systems carrying confidential data are exposed to security attacks. By the wireless’s nature within these networks, they become susceptible to different kinds of attacks, hence, it seems essential to design the appropriate safety mechanism in such networks. The sinkhole attack is one of the most dangerous and threatening attacks amongst types of attack in UAS. A malicious UAV exists in such a threat attacking as a black hole for absorbing all traffic in the network. Mainly, in a Flow-based protocol, the attacker considers the requests on the route, then, it replies to the target UAV such as high quality or the best route towards Gard station. The malicious UAV is able to only insert itself on one occasion between the nodes relating to each other (such as sink node and sensor node), and act for passing packets among them. In this study, the malicious attacks are detected and purged using two stages were. In the first stage, some principles and rules are used to detect black hole, gray hole, and sinkhole attacks. In the second stage, using a smart agent-based strategy negotiation procedure for three steps, a defense mechanism is designed to prevent these attacks. The smart agent is used by reliable neighbors via the negotiation procedure for three steps, hence, the traffic formed by the malicious UAV is not considered. The suggested protocol is called SAUAS. Here, the technique is assessed through extensive simulations performed in the NS-3 environment. Based on the simulation outcomes, it is indicated that the UAS network performance metrics are enhanced based on the packet delivery rate, detection rate, false-negative rate and false-positive rate.