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There's a World Buddhist Directory which may be helpful (I don't know any personally).
This URL -- http://www.buddhanet.info/wbd/search.php?keyword=&search=Search&country_id=42&province_id=0&tradition%5B%5D=mahayana -- returns 35 "Mahayana" matches in India, and several of these are Zen (or probably Zen even if they don't say "Zen").
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There is a Zen Ashram near Kodaikanal called - Bodhi Zendo Ashram. Goolge it, you will find the website and location along with contact detials.
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There is a temple associated with Sogenji and Shodo Harada of the Rinzai sect in India: Indozan Sogenji.