Israeli Transportation Minister Israel Katz said an agreement to restart the flights was signed this week after months of negotiations, Hurriyet Daily News reported Thursday.
Scheduled and charter flights to Turkey had stopped because of Israeli concerns about security at the airports at which the planes landed.
The agreement resolves those concerns, with Israeli officials saying Turkey had given them satisfactory answers and solutions.
Giora Romm, director-general of the Israeli Civil Aviation Authority, said flights are expected to resume by next summer.
Turkish Airlines has 60 flights into Israel each week.
Relations between Turkey and Israel have been in a slump in recent years, with the most recent decline in 2010 caused by Israeli forces raiding a Turkish aid vessel, the Mavi Marmara, as it tried to break the Gaza blockade, Today's Zaman reported.
Israeli Environmental Affairs Minister Amir Peretz signaled early this month relations between the countries might be on the mend.
After meeting with Turkish officials on the sidelines of a U.N.-sponsored conference in Istanbul, Peretz said he believes "in the very near future, we can solve the problems between Turkey and Israel. Turkish and Israeli citizens want their governments to achieve reconciliation as soon as possible."