ISTANBUL  The Israeli commando raid on Monday on an aid flotilla, which left at least nine people dead, has dragged relations between Israel and Turkey to a new low, political experts here say, threatening to derail diplomatic relations between two close American allies.

Turkey, a NATO member, has long been Israel’s closest friend in the Muslim world, with $2.5 billion in trade in 2009 and strong ties between the countries’ militaries and governments. But relations began to deteriorate during Israel’s war in Gaza, when Turkey’s prime minister, Recep Tayyip Erdogan, publicly sparred with Israel’s president, Shimon Peres, at the World Economic Forum in Davos, Switzerland.

Monday’s raid on the Gaza-bound aid flotilla, which was sponsored in part by a Turkish organization, prompted street protests in Turkey and a strong official reaction, with Ankara recalling its ambassador from Israel, summoning Israel’s ambassador and canceling planned joint military exercises. That was enough to raise alarms among analysts here, who said it could seriously jeopardize already battered diplomatic relations between the countries.

“This will be perceived as a kind of declaration of war on Turkey,” said Cengiz Candar, a columnist for Radikal, a Turkish daily. “Political dialogue will cease. It’s not possible to contain the deterioration in relations anymore.”