Reuters had reported in June that Watsa's firm was set to take a 70 to 75 per cent stake in NCMSL worth $120 million to $150 million.
The deal, valued at about Rs 800 crore, is expected to be completed in 2015, Fairfax said in a statement.
NCMSL, which is hoping to benefit from a boost to India's underdeveloped agricultural storage industry under Prime Minister Narendra Modi's push for food security, will continue to operate independently under Chief Executive Sanjay Kaul, Fairfax said.
Hyderabad-born Watsa, whose main firm is Fairfax Financial Holdings, set up Fairfax India late last year to boost the firm's investment in India. Fairfax India went public in January this year and raised more than $1 billion via its initial public offering. ($1 = Rs 63.64)
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