Whitaker has been an England selector for 10 years and his departure is linked to the ECB's introduction of a formalised scouting network to pick its test, Twenty20 and one-day sides.
The system includes a three-strong selection panel consisting of Whitaker's replacement as national selector, a full-time independent England selector and the England head coach.
This panel will receive information on players from a team of designated discipline-specific scouts in a bid to give selectors deeper insights into the available talent pool.
"The new approach will allow us to see more players throughout the county game, more often, and simplify the selection process," England cricket director Andrew Strauss said in a statement.
Whitaker has overseen four Ashes series wins, victory in the 2010 World Twenty20 in 2010 and test series triumphs in India and South Africa.
"It has been an immense privilege and an honour for me to have been an England selector for the last 10 years," he said.
"I have been involved for a decade now and it feels that the time is right, with this new approach, for me to move on."
The ECB aims to appoint Whitaker's replacement by mid-May, when the squad for the home test series against Pakistan is named.
(Reporting by Simon Jennings in Bengaluru, editing by Ed Osmond)
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