The former Australian Test batsman, 53, will take over as director of operations at the Bangalore-based National Cricket Academy later this month, the academy's newly-appointed chairman Ravi Shastri said on Wednesday.
"I am glad to have Whatmore on board because he is one of the best in the business," said Shastri, an ex-India captain and noted television commentator.
"He will be at the academy for three years."
Whatmore, who shot to fame after masterminding Sri Lanka's World Cup win in 1996 and served Bangladesh with distinction for four years, was seen as the likely choice for the India job when Greg Chappell quit after the World Cup.
But Indian officials did not even invite Whatmore for an interview and are still hunting for a permanent coach after South African Graham Ford declined to accept their offer.
Whatmore, who was also overlooked by Pakistan following the death of their national coach Bob Woolmer, said he looked forward to working at the academy.
"It did not tak