"The executions in Saudi Arabia are an internal legal matter. Whether you approve or not of the decision is a separate issue," Erdogan said in a televised speech, his first reaction to the controversy which has raised tensions between Saudi Arabia and its regional rival Iran.
Erdogan had last month visited Riyadh for talks with King Salman and the political elite, in a new sign of Ankara's warm ties with the kingdom.
Meanwhile, tensions have increased between Turkey and mainly Shiite Iran, which along with Russia is the key remaining ally of Assad.
The crisis began at the weekend when Saudi Arabia executed prominent Shiite cleric and activist Sheikh Nimr al-Nimr as well as 46 other convicts, prompting a furious reaction from Tehran.
Iranian protesters then ransacked the Saudi embassy in Tehran. Riyadh, Bahrain and Sudan severed relations with Tehran while Kuwait recalled its ambassador.
"Only three (of those executed) were Shiites," said Erdogan.
He also questioned also "why the world did not react" to the condemnation of "thousands of people to death" following the ousting in Egypt of former president Mohamed Morsi, an ally of Ankara.
Prime Minister Ahmet Davutoglu on Monday urged Iran and Saudi Arabia to calm tensions, saying the hostility between the two key Muslim powers would only further escalate problems in an explosive region.
But Erdogan's comments contrasted with those Monday by Turkish Deputy Prime Minister Numan Kurtulmus, who is also government spokesman, that "death penalties, especially ones that are politically-motivated, are of no help to making peace in the region."
