In regards to the Cyprus situation, he was faced with three options. The first was to go to war with Turkey. But the Greek dictators, paradoxically, had kept Greece militarily exposed by leaving the Aegean Islands undefended against a possible Turkish military operation. The second option was to seek a truce so as to gain time and later begin a massive rearmament that would enable Greece to push the Turks out of Cyprus at an opportune moment. Had this option been chosen, Greece and Turkey likely would have initiated a chain reaction of revanchist wars similar to those that occurred between Israel and its Arab neighbors. The result of that decision would have been a climate of high tension that would have prevented Greece from securing membership in the EC. The third option was to arm Greece for purposes of adequate deterrence of future Turkish expansionism in Cyprus, the Aegean, and Thrace, while at the same time applying political, economic, and diplomatic pressures to promote a viable settlement in Cyprus and the Aegean.

Karamanlis took the third option, believing that at that point Greek national security required maximum integration into the European Community, even though from the Greek viewpoint that course meant abandoning certain territorial and nationalistic goals. Although Greece subsequently withdrew from the military structures of NATO in protest against perceived Western failure to prevent the Cyprus "invasion," Karamanlis's decision set an important precedent for Greek national security policy for the ensuing twenty years.

Punishing the junta and reforming the military and the civil service were more delicate operations. Karamanlis wanted to avoid a repetition of the military retributions of the 1920s and to preserve relations between the civilian government and the military.