Deutsche Welle has lodged a protest with Baghdad's embassy in Berlin, a statement from the broadcaster said.
Officials at Iraq's interior ministry and the state body overseeing media did not respond to enquiries by AFP on Friday.
Jaafar Abdul Karim, a German of Lebanese origin who hosts the hugely popular "JaafarTalk" programme, had been due to record an episode in Baghdad. The focus was to be on "youth unemployment, political participation and women's rights", the DW statement released late Thursday said.
Representatives of the 2019 protest movement in Iraq had been scheduled to take part, along with government officials.
But DW said its team "came under increasing pressure from high-ranking Iraqi officials" after one media outlet "published a video on Instagram accusing the DW presenter of trying to spread 'abnormal and perverted' sexual behaviour in Baghdad".
Previous episodes from JaafarTalk had been about homosexuality.
The German broadcaster said the weekly programme "tackles topics deemed taboo in the region".
DW said the authorities "suddenly demanded a special filming permit for the planned recording despite having applied for and been granted the usual permits in advance".
It said ministry representatives visited the team's hotel late Wednesday to tell Abdul Karim that he was not allowed to work without special permission "and could face arrest if he did not comply".
The government could not guarantee his safety, they added.
DW said the team left the country the following morning.
"It is alarming how journalists are being treated in Iraq," DW chief editor Manuela Kasper-Claridge said in the statement.
"The threat to our team and host Jaafar Abdul Karim by forces in Iraq who want to put a stop to free speech is unacceptable."
The broadcaster said its protest note to Iraq's embassy in Berlin called the incident "an unprecedented restriction of press freedom".
Iraq ranks 172 out of 180 in the Reporters Without Borders (RSF) barometer of the most dangerous countries for journalists.
Last June, the United Nations mission in Iraq deplored what it called an "environment of fear and intimidation" limiting freedom of expression.
The 2019 uprising was bloodily repressed, with dozens of activists becoming victims of murder, attempted murder or kidnap.
Abdul Karim gave an impassioned response on Twitter Friday. "You can't (threaten) a whole generation that believes in Human Rights and Freedom! We will continue our Dialogue!"
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