The Turkish Foreign Ministry on Wednesday told Israel's consul general in Istanbul Yosef Levi Sfari to leave the country "for a while".
It rejects the criticism, saying its open-fire rules are necessary to defend its border.
Turkey has expelled Israel's ambassador and recalled its ambassadors from Tel Aviv and Washington.
Israel's Foreign Ministry said the Turkish Consul-General in Jerusalem had been summoned and told to return to Turkey "for consultations for a period of time".
At least 62 Palestinian demonstrators were martyred and hundreds more injured by Israeli armed forces along the Gaza border Monday, according to the Palestinian Health Ministry.
Ankara has reacted with fury to the killing of at least 61 Palestinians in Gaza on the same day as the USA formally moved its embassy in Israel to Jerusalem from Tel Aviv in defiance of global outrage.More news: Two Useless, Cars and Trucks Burnt In Aurangabad Clashes, Prohibitory Orders Imposed
"Erdogan is one of the biggest supporters of Hamas, so there's no doubt he's an expert on terror and slaughter", Netanyahu said in a Hebrew-language Twitter post.
After talks with British Prime Minister Theresa May on Tuesday, Erdoğan warned that history "will not forgive" Israel or the United States for moving the American embassy to Jerusalem in defiance of the Islamic world.
Israel suspended the import of agricultural products from Turkey on May 16.
Prime Minister Binali Yildirim earlier said Turkey is calling on Muslim countries to reconsider relations with Israel.
The Organization of Islamic Cooperation has strongly condemned the Israeli aggression against Palestinian civilians, which led to the martyrdom of more than 52 and the injuries to about 2,000 people during peaceful protests.