Eight people, including members of the security forces, were reported to have died in clashes in the northern city of Marsa Matrouh.
Casualties were also reported in the port city of Alexandria, Minya in southern Egypt and Fayoum, south of Cairo.
The violence came after the army announced on Wednesday that Morsi was no longer president.
Moreover, the US embassy in Cairo has ordered the evacuation of all non-essential personnel and diplomats' family members because of political unrest in Egypt, the State Department said Wednesday.
In a travel warning to US citizens, the State Department also warned against travel to Egypt and urged Americans to leave the country, it warned unrest was "likely to worsen in the near future."
The embassy had been closed Wednesday amid mass protests and had been due to be closed Thursday.