Turkish President Recep Tayyip Erdogan on Tuesday lashed out at the satirical magazine, calling its move a "vile provocation".
As protests erupted in Istanbul, the magazine's top editor said the image had been misinterpreted and was "not a caricature of Prophet Mohammed (PBUH)".
"We will not allow anyone to speak against our sacred values, no matter what," Erdogan said in televised remarks.
"Those who show disrespect to our Prophet and other prophets will be held accountable before the law," he added.
Erdogan said the authorities had seized all copies of the offending issue and were taking legal action against the publication.
The Turkish president's comments amplified a wave of official condemnations a day after four cartoonists at the LeMan magazine were detained over the drawing.
The cartoon, published a few days after the 12-day Israeli aggression on Iran, has been interpreted as showing Prophet Muhammad (PBUH) and Prophet Moses (AS), shaking hands in the sky over a wartime scene.
It was also criticized by religious figures, even as the magazine apologized to readers who felt offended and said it had been misunderstood.
The magazine's editor-in-chief Tuncay Akgun told AFP by phone from Paris that the image had been misinterpreted and was "not a caricature of Prophet Muhammad".
"In this work, the name of a Muslim who was killed in the bombardments of Israel is fictionalized as Mohammed. More than 200 million people in the Islamic world are named Mohammed," he said.
The cartoon had "nothing to do with Prophet Muhammad (PBUH)," said Akgun, adding, "We would never take such a risk."
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More than 200 people arrived to protest against LeMan in central Istanbul on Tuesday, despite a ban on gatherings and heavy police presence.
Turkey's ruling AKP party also condemned the cartoon earlier Tuesday. "This has nothing to do with art, ideas, freedom of expression, or artistic freedom," said AKP spokesman Omer Celik.
"In our view, this is a hate crime — an act of hostility directly targeting Islam, Prophet Moses, and our Prophet."
In a statement on X, LeMan said "the work does not refer to the Prophet Muhammad in any way".
The cartoonist, Dogan Pehlevan, had sought to highlight "the suffering of a Muslim man killed in Israeli attacks", it said, adding there was no intent to insult Islam or its prophet.
The magazine urged authorities to counter what it called a smear campaign, and to protect freedom of expression.
Source: France24