The move comes after days of mass street demonstrations against Mr Mursi's rule and an ultimatum issued by the military which expired on Thursday without being heeded.
The army's intervention is supported by millions in Egypt, including liberal leaders and religious figures who expect new elections under a revised set of rules.
The Ministry of Foreign Affairs says there are 201 New Zealanders registered as being in Egypt.
Prime Minister John Key said on Thursday that the country is going through a challenging process of transferring to democracy which he hopes can be resolved peacefully.
Mr Key said unless people urgently need to go to Egypt, they should avoid doing so. However, he is confident New Zealand diplomats at its embassy in Cairo are safe and at this stage there is no need to evacuate them.