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I have done by B.Tech in Biotechnology couple of years ago. Since then I am working with a company on bioinformatics research. I also did 1 year PG Diploma in Bioinformatics from classroom program.

Most of the Indian and UK universities have this prerequisite that I need to have a masters degree for PhD. As I am currently working in a company, will correspondence or distance learning masters will be valid?

I already saw these:

Distance learning: taken seriously?

Are Master's becoming required for USA PhD programs?

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Skipping the reputation aspects discussion, programs and degrees from any nationally accredited higher education institutions are all valid. In US, such institutional accreditation comes in a form of an accreditation from one of several regional commissions, such as Southern Association of Colleges and Schools Commission on Colleges (SACS-COC). I imagine that similar accreditation mechanisms exist in UK, India and most other countries. Keep in mind that there is a significant difference in the educational process and its outcomes, as well as, consequently, your future career prospects, between nationally accredited programs and degrees and the unaccredited ones. For more information, see this Wikipedia article as well as articles linked in the its "See Also" section.

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