After a long search i finally found a few Zen Centers in India. Turns out Zen is extremely rare in India, I don't understand why that is the case. I think Some International Schools must take initiatives to set up centers here.

1.Bodhi Zendo,
is located in South India. (please visit their website for knowing more)
http://www.bodhizendo.org/
Bodhi Zendo is situated in Tamil Nadu, South India, in the upper Palani Hills at an altitude of about 1700 m, about 100km north-west of Madurai (National Airport). The nearest village is Perumalmalai and the nearest town, the hill resort of Kodaikanal. The closest International Airports are Chennai/Madras, Bangalore or Trivandrum.

2.Open Dharma
Lucknow, Uttar Pradesh, India
Contact: Jaya Ashmore
Email: towardsliberation@yahoo.com
Web site: http://www.opendharma.org
Tradition: Buddhist vipassana (insight),
Zen and metta meditation traditions.
Teachers: Jaya Ashmore and Ajay Singh

To know about other Buddhist Centers in India visit this link
http://www.dharmaweb.org/index.php/India