During his tenure as Patriarch, more friction arose with the Hierarchs of Sinai, who continued to perform religious ceremonies at the Sinai Dependency of Cairo, without the essential permission of the Patriarch of Alexandria. When Nikiphoros was away in Moldovlachia they attained the relative permission from the Ecumenical Patriarch Parthenios I, who was later forced to retract it, following a protest by Patriarch Nikiphoros and the intervention of Basilios, governor of Moldovlachia. He fell asleep unexpectedly in April 1645.