The attainment of security level in telemedicine communication systems might be a sensitive research area because of its content confidentiality. The proposed Intrusion Detection System (IDS) research work presents a model for detecting attempts of attacks to acquire unauthorised access to a web based telemedicine system. The process of attacks detection would be performed by applying Conditional Random Field (CRF) based approach because of its structured prediction feature. The proposed mechanism deals with structured prediction approach and hence it is suitable for identifying the attacks over the web based telemedicine application. From the experimental observations, the proposed scheme offers high efficiency with accuracy in terms of detecting the attacks (Probe, R2L, U2R and DoS). This model presents proficient results over the medical data communication in terms of efficient attack detection time, false alarm rates along with good classification accuracy.