The court in Istanbul will ask Interpol to issue international arrest warrants for four men involved in a deadly raid on a Gaza-bound aid ship, Cihat Gokdemir, a lawyer working on the case, told AFP.
The ruling is part of an ongoing criminal trial in absentia of the four men on charges brought by aid group IHH and the victims' families in 2012, which has been denounced as a "show" by Israel.
An Israeli official, speaking on condition of anonymity, described the court's decision today as a "ridiculous provocation".
"If this is the message that the Turks want to send to Israel, it was perfectly well understood," said the official, declining to elaborate further on what this meant for the reconciliation process.
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Turkish officials recently said they were close to a deal that would see Israel pay compensation for the deaths. Local media said Israel had insisted any deal be conditional on the lawsuits against the soldiers being dropped.
Nine Turkish activists died aboard the Turkish-flagged Mavi Marmara, the largest ship in a flotilla dispatched by Turkish relief agency Humanitarian Relief Foundation (IHH) to break Israel's blockade of the Gaza Strip, on May 31, 2010.