Hazrat Miran Syed Muhammad Mahdi al-Mau'ood (AS) has prohibited his followers from saying their prayers in the leadership (imamat) of munkirs (non-believers). He has also said that if any of his followers had said his prayers by mistake in the leadership (imamat) of a non-believer, he should say his prayers anew.
(Insaaf Nama - Matan Sharif, N.1)