National media have been reporting today that the MP for the Calder Valley stepped down from the post in February in protest to Chris Pincher being appointed to help oversee party discipline.
Chris Pincher has this week had the Conservative whip suspended following allegations he groped two men at a members club in London.
But in a statement, Mr Whittaker has said: “Following press speculation I want to clarify that I left the Whips' Office in February 2022 due to health issues I was experiencing at the time."
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Mr Whittaker told the Courier at the time of his resignation that he was stepping down for personal reasons.
The Conservative is still MP for the Calder Valley, a role he has held since 2010.
Whips are MPs or Lords appointed by each party in Parliament to help organise their party's contribution to parliamentary business.
One of their responsibilities is making sure the maximum number of their party members vote, and vote the way their party wants.