Interior Ministry jets dropped leaflets on sit-ins at Rabea al-Adaweya and al-Nahda Square in Cairo on Sunday, warning protesters to leave.
Leaflets claimed the ministry was "aware" protesters in both sit-ins have been "brainwashed" by the Muslim Brotherhood.
The ministry also warned against continuing the sit-ins, claiming their organizers are implicated in incidents of murder, torture, child abuse and incitement to violence.
Protesters, supporting deposed President Mohamed Morsy, have been staging sit-ins at Rabea al-Adaweya Square for 39 days and at Nahda Square for 34 days demanding his return to power.
The ministry earlier called on Morsi’s supporters to evacuate the squares for their safety, assuring them of a safe exit.
A series of warnings from the Interior Ministry suggest police could surround and possibly disperse the protest sit-ins at an undisclosed date.