Turkey now regards Israel as a "major threat" to its security.
According to Turkish newspapers, the country's National Security Council made the assessment last week in its new five-yearly strategic report.
The security agency took four of the country's neighbours, Syria, Bulgaria, Armenia and Georgia, off the list. Greece, which recently began carrying out joint military exercises with Israel, remains on the threat list.
Two years ago, Turkey regarded Israel as a strategic ally in the Middle East but the pro-Islamist government headed by Prime Minister Reccep Tayyep Erdogan began changing its alignment following Operation Cast Lead in Gaza at the end of 2008. Relations took a further nose-dive following the flotilla incident six months ago.
The reason given for Israel's inclusion in the threat list was that its actions could lead to an "arms race" in the Middle East. The Israeli government refused to respond to the report.