Finance Minister Arun Jaitley said in a Twitter post that the government appreciated all of Rajan's good work and respected his decision
The system will wed BlackBerry's security platform with the South Korean company's own security software for its Galaxy devices.
The company plans to raise $1 billion with a private placement of convertible debentures.
The device has already garnered good reviews, which helped RIM stock surge.
Experts believe that Canadian govt might make it difficult.
RIM shares up more than 3 pct on Nasdaq and TSX.