Flying Ad Hoc Networks (FANETs), which primarily interconnect Unmanned Aerial Vehicles (UAVs), present distinctive security challenges due to their distributed and dynamic characteristics, necessitating tailored security solutions. Intrusion detection in FANETs is particularly challenging due to communication costs, and privacy concerns. While Federated Learning (FL) holds promise for intrusion detection in FANETs with its cooperative and decentralized model training, it also faces drawbacks such as large data requirements, power consumption, and time constraints. Moreover, the high speeds of nodes in dynamic networks like FANETs may disrupt communication among Intrusion Detection Systems (IDS). In response, our study explores the use of few-shot learning (FSL) to effectively reduce the data required for intrusion detection in FANETs. The proposed approach called Few-shot Federated Learning-based IDS (FSFL-IDS) merges FL and FSL to tackle intrusion detection challenges such as privacy, power constraints, communication costs, and lossy links, demonstrating its effectiveness in identifying routing attacks in dynamic FANETs.This approach reduces both the local models and the global model's training time and sample size, offering insights into reduced computation and communication costs and extended battery life. Furthermore, by employing FSL, which requires less data for training, IDS could be less affected by lossy links in FANETs.