With the development of next-generation sequencing technology, a massive amount of genomic data are being generated day by day. To efficiently handle these data for storage, processing and transmission, some specialized genomic data compression techniques are need of today. In the near future, personalized genomics may come into existence where doctors may give the treatment on the basis of patient genome. It creates a huge challenge to securely store and transmit the genomic data over the cloud servers or remote servers. This problem can be solved by applying a combination of encryption and compression techniques. Most of the state of the art algorithms for secure and efficient storage of genomic data adopt the policy of encryption after compression. The computational costs of these algorithms are very high, so there is a need to develop a unified encryption-compression algorithm (encryption during compression) to provide the confidentiality/secrecy also to genomic data. In this paper an approach applying encryption during compression is proposed to efficiently and securely store the genomic data in fasta/multi-fasta file format. Here MWBTC (Modified Word Based Tag Code) and Delta Encoding are used for compression and AES-256 is used for encryption. Experiments show that the proposed algorithm (WBMFC) outperforms the state of the art algorithms in terms of processing time and compression ratio both.