"Security forces raided the house of Al-Musalami al-Kabbashi, the Al Jazeera bureau chief in Sudan, and detained him," the network said on Twitter without elaborating.
Al Jazeera has given prominent coverage to demonstrations against the 25 October coup but last week it also aired a detailed interview with top general Abdel Fattah al-Burhan, one of only two he has granted.
The protests, including by tens of thousands of people nationwide on Saturday, have continued despite a rigorous internet outage forcing demonstrators to communicate via graffiti and SMS messages.
Other media outlets besides Al Jazeera have also been targeted since the coup, when Burhan declared a state of emergency, detained the civilian leadership and removed the government installed after the April 2019 military ouster of autocratic president Omar al-Bashir.
Burhan, de facto head of state since Bashir fell, has sacked the head of Sudan's state television, Luqman Ahmed, a veteran advocate of civilian rule.
The head of the official news agency SUNA was also fired after soldiers seized the premises and forced journalists out, according to reporters.
In another change, leadership of the council which grants work licences for local and international media reverted to Abdelazim Awad, who led the council during Bashir's rule.
Broadcasts on multiple private radio channels have also been suspended, according to reporters working there. The coup has triggered wide global condemnation and punitive measures by Western countries and the World Bank.
Ahead of the latest rallies the United Nations called on security forces to show restraint, in a country where more than 250 people had already died in mass protests leading to Bashir's ouster.
Since the coup, 21 more have been killed in demonstrations, according to an independent union of medics. The union said that figure includes six more who died Saturday. Five were shot dead while one died from "suffocation by tear gas", the medics said.
The US embassy in Khartoum said it regretted the loss of life and injuries "of dozens of Sudanese citizens demonstrating today for freedom and democracy."
Gunshots were heard and tear gas fired as security forces tried to break up the protests, witnesses and AFP correspondents said.
Police denied using "live rounds" and said 39 of their personnel were "severely wounded" in confrontations with the protesters whom they accused of attacking police stations.
Hundreds of people also demonstrated in Europe and in Washington, DC, to support the Sudanese who have remained undeterred despite the deadly toll and arrest of hundreds.
In a statement, Al Jazeera condemned "in the strongest terms the reprehensible actions of the military and calls on the authorities to release al-Kabbashi immediately", and to allow its journalists to operate unhindered without fear or intimidation.
By Sunday morning, the streets of Khartoum and neighbouring cities were largely open and traffic flowed as usual. Bridges into the capital which were sealed off Saturday had reopened.
The demonstrations came two days after Burhan, despite calls by the West, Saudi Arabia and the United Arab Emirates for a return to the civilian-led transitional government, announced a new civilian-military ruling council with himself as head.
It excludes any members of the Forces for Freedom and Change, an umbrella alliance which spearheaded the anti-Bashir protests, and was the main bloc seeking a transition to civilian rule.
The alliance called for more large-scale protests on Wednesday. Burhan insists the military's move on 25 October "was not a coup" but a push to "rectify the course of the transition".