Israel has refused to sell Turkey anti-tank missiles, armored personnel carriers and naval anti-aircraft missile systems. Israel is completing earlier Turkish purchases of weapons, but will not sell new ones because of the growing anti-Israel attitudes of the Turkish government.
The Islamic politicians now running Turkey are trying to overcome objections by their own military, and cut all military cooperation with Israel. The Islamic politicians want to do this to improve their stature in the Islamic world. The military wants to maintain the relationships because it increases Turkish combat power. This is seen as important, given the growing ambitions of neighboring Iran, and the possibility that Iran will soon have nuclear weapons, and more confidence about threatening Turkey. The Turks and Iranians have been rivals, and often at war, for over a thousand years. But now Turkey is cozy with Iran, and it is feared that Iran would be given Israeli military equipment for examination.
Despite all this, Israel and Turkey continue to cooperate in some areas. For example, Israel recently thanked Turkey for assistance in preventing Hezbollah from attacking Jews in Turkey. There are several Islamic radical groups operating in Turkey, and their terror attacks (usually against government targets) make the public angry, and nervous about their safety. Israel and Turkey continue to cooperate in tracking Islamic terrorists, and sharing information. Turkish Islamic politicians are willing to continue with this, as long as it is kept quiet. Similar arrangements have long been maintained between Israel and many Islamic nations.
Since the 1990s, when Turkish Islamic political parties began winning elections (on the promise of using Islam to cure problems with corruption and economic stagnation), these Islamic parties became more powerful. By 2002, Islamic parties were running the government, and made good on their pledge to improve the economy. But they also became anti-Israel, and now Israel has responded by cutting off the supply of military gear. Turkey can buy similar stuff elsewhere, but loses the advantage of having a neighbor, with a strong military, as an ally.