On Saturday, Sri Lanka's former batting coach Jon Lewis had to pull out from the coaching role.
Whatmore was earlier named as a coach for the Colombo Kings team.
He will be replaced by another foreigner.
"Whatmore has pulled out for some personal reasons. England's Kabir Ali will take his place", a source in Colombo, said exclusively.
Former right-arm fast bowler Kabir Ali played 1 Test and 14 ODIsand has 25 international wickets to his credit.
Angelo Mathews will be the captain.
Local Sri Lankan players are likely to join the camp on Monday and foreign players including Daniel Bell-Drummond and Laurie Evans (both England), West Indies' Andre Russell, and India's Manpreet Singh Gony from England, Dubai and India will join on 18th November.