'Co-operating with Israel'
"The change will come when the Turkish people urge their government to stop co-operating with Israel ... or taking part in killing Muslims in Afghanistan," he said, referring to Turkey's participation in the Nato mission in the country.
Turkey, Israel's strongest Muslim ally prior to the flotilla raid in May which killed eight Turkish activists and one Turkish-American, has demanded an apology from Israel for the deaths.
So far, Israel has refused to do so, severely damaging relations between the two former-friends and US allies.
"The Turkish government issues statements against Israel, but at the same time commits the same Jewish crimes against the Muslim mujahideen in Afghanistan, burning their houses, demolishing their villages and even assuming the leadership of Nato there," al-Zawahiri said.
He said the siege on Gaza demonstrates what he called the Zionist Crusader campaign, aided by "Arab traitors" and the United States.
Al-Zawahiri, who has a US bounty of $25m on his head, made is last known public statement in July, when he criticised Barack Obama, the US president, for launching "a new stage in the Crusader and Zionist campaign".