The Conservative was appointed as a Lord Commissioner of HM Treasury yesterday.
Mr Whittaker has been a whip previously but resigned in February, citing personal reasons.
National media reported last weekend that Mr Whittaker had left in protest to Chris Pincher - the MP at the centre of groping allegations - being appointed to help oversee party discipline.
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But Mr Whittaker, following the stories, released a statement saying he wanted to clarify that he left because of health reasons he was suffering at the time.
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.
The Whips Office has said it will stay neutral throughout the Conservative Party leadership contest and aim to ensure the smooth running of Parliament and Government.