In one of his most vehement broadsides ever against the Jewish state, Erdogan also announced three days of national mourning over the deaths, as well as a giant protest in Istanbul on Friday.
"What Israel has done is a genocide. I condemn this humanitarian drama, the genocide, from whichever side it comes, Israel or America," he added.
Violent clashes erupted along Gaza's border as the US opened its Israel embassy in Jerusalem in a ceremony attended by a White House delegation and Israeli officials. Erdogan and other Turkish officials have repeatedly condemned the US decision to move the embassy, warning it risked inflaming tensions.
The Turkish president announced he was calling a "giant meeting" on Friday to protest Israel's actions at the vast Yenikapi area in Istanbul, which has capacity for more than a million people.
Erdogan regards himself as a champion of the Palestinian cause and last year held a summit of Islamic countries to denounce US President Donald Trump's decision to recognise Jerusalem as Israel's capital.
However Turkey also maintains full trade and diplomatic links with the Jewish state after a 2016 reconciliation deal ended a dispute over the deadly storming of a Turkish ship by Israeli commandos.
"The United States, unfortunately, took its place without complaint alongside the Israeli government in this massacre of civilians and became a party to this crime against humanity," Prime Minister Binali Yildirim said.
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