Pairings on elliptic curves have been used as cryptographic primitives for the development of new applications such as identity based schemes. For the practical applications, it is crucial to provide efficient and secure implementations of the pairings. There have been several works on efficient implementations of the pairings. However, the research for secure implementations of the pairings has not been thoroughly investigated. In this paper, we investigate vulnerability of the pairing used in some pairing based protocols against side channel attacks. We propose an efficient algorithm secure against such side channel attacks of the eta pairing using randomized projective coordinate systems for the pairing computation.