Distributed Computing system is a cluster of computers connected on a network which coordinate their actions via passing messages. Since the cluster can also be accessed publicly, the security of various messaging operations is of great concern. In this paper a highly efficient and secure implementation of message passing interface (MPI) in distributed environment has been proposed and implemented. This implementation, which is named as VAN-MPICH2, integrates security measures to ensure data confidentiality using One-Time Pad (OTP) encryption technique. Since the proposed encryption implementation decreases the security overhead substantially, VAN-MPICH2 manages to provide confidentiality with very insignificant decrease in performance.