The court will ask Interpol to issue international arrest warrants for the four men, lawyer Cihat Gokdemir told AFP.
No one at the Israeli embassy in Ankara was immediately available for comment.
Turkish prosecutors are seeking life sentences for the commanders, who went on trial in absentia in 2012.
They are former military chief of staff Gaby Ashkenazi, former navy chief Eliezer Marom, former military intelligence head Amos Yadlin and former air force intelligence chief Avishai Levy.
Israeli commandos boarded the Turkish-flagged Mavi Marmara, the largest ship in a flotilla dispatched by Turkish relief agency IHH to break Zionist regime’s blockade of the Gaza Strip, on May 31, 2010, leaving nine Turkish activists dead.
The assault sparked widespread condemnation and provoked a major diplomatic crisis between the two countries.
Ankara expelled the Israeli ambassador, demanded a formal apology and compensation.
IHH together with the victims' families brought a criminal case against the four Israeli ex-military chiefs after the maritime assault.
An Israeli probe ruled that the raid did not violate international law, in a finding that Turkey said lacked credibility.
Talks on compensation began a year ago after Israel extended a formal apology to Turkey.
Authorities had said recently they were close to a deal that would see Israel pay compensation for the deaths, but Tel Aviv said this was conditional on the lawsuits against its officers being dropped.
NJF/NJF