Downing Street has told PinkNews that Nicky Morgan will report directly to the Prime Minister and not the new Equalities Secretary Sajid Javid.
In a government reshuffle on Wednesday, sparked by the resignation of Maria Miller, Ms Morgan was appointed Financial Secretary to the Treasury and also Minister for Women.
Her appointment has generated surprise and criticism.
But unlike Ms Morgan, Mr Javid, voted in favour of the same-sex marriage act for England and Wales.
The joint ministerial portfolio of women and equalities has now been separated.
Downing Street told PinkNews the move reflected David Cameron’s desire to take a greater interest in women’s policy across government.