The government of Ivorian President Alassane Ouattara blamed Ghanaian allies of former President Laurent Gbagbo for attacks in the West African country. The country closed its borders with Ghana last week after gunmen attacked a military checkpoint in a border town.
Ouattara's office was quoted by the BBC as saying the air borders were reopened following "48 hours of observation of the movements of people and goods between the two countries."
Gbagbo was transferred to the International Criminal Court following his arrest in April 2011. Rival claims to the presidency in 2010 pushed the country to the brink of civil war. Human rights groups suspect both sides committed atrocities during the post-election crisis.
The United Nations last month said it was "carefully reassessing" the security situation in the country following a series of attacks near the commercial capital Abidjan. Ouattara's office said land and maritime borders with Ghana would remain closed for the time being.