German federal police confirmed a 52-year-old journalist travelling to Doha had been arrested at Berlin Tegel airport.
"I am still under arrest at Berlin airport, waiting to be taken before an investigating judge," Mansour wrote on his Twitter account.
A police spokesman said the arrest took place at around 3:20 pm (1520 GMT) adding that while Mansour was born in Egypt, he also has British nationality.
By Saturday evening the journalist was still in police detention and was set to be taken before a judge, who would determine whether an extradition process would be launched, the spokesman added.
The Egyptian-issued arrest warrant accused Mansour of committing “several crimes", German police said, without giving further details.
Doha-based Al-Jazeera confirmed the arrest, and called for his immediate release.
"The crackdown on journalists by Egyptian authorities is well known. Our network, as the Arab world's most-watched, has taken the brunt of this," said the network's acting director general Mostefa Souag in a statement.
"Other countries must not allow themselves to be tools of this media oppression, least of all those that respect freedom of the media as does Germany. Ahmed Mansour is one of the Arab world’s most respected journalists and must be released immediately," he added.
Al-Jazeera also said on its website that an Egyptian court had sentenced Mansour in absentia in 2014 to 15 years in prison, for "torturing a lawyer in 2011 on Tahrir Square" in Cairo, epicentre of an anti-regime uprising that brought down former president Hosni Mubarak.
"Mansour has rejected these absurd accusations," the network said.
Still detained, Mansour tweeted: "The question now is how have the German government and Interpol become tools in the hands of a bloodthirsty regime in Egypt that came to power through a coup, and is led by the terrorist (President) Abdel Fattah al-Sisi.”
Mansour, who hosts a popular news interview programme, recently interviewed Abu Mohamed al Jolani, the chief of Al-Qaeda's Syria affiliate, Al-Nusra Front.
Ties between Doha and Cairo have been extremely strained over Qatar’s backing for the former, short-lived Egyptian government under the Muslim Brotherhood.
Three Al-Jazeera journalists in Egypt, including Canadian Mohamed Fahmy and Australian Peter Greste, were arrested in 2013 and then sentenced to up to 10 years in prison on charges of supporting the Muslim Brotherhood.
Greste has since been deported while the other two are facing retrial.
Egypt's Sisi visited Germany on June 3, as prominent rights groups urged Chancellor Angela Merkel to press him to end "the gravest human rights crisis in Egypt in decades."