The Arab satellite channel's Khartoum bureau was searched on Wednesday and broadcasting equipment was confiscated despite police being supplied with legal documents and broadcasting permits.
Islam Salih, Aljazeera's Sudan bureau chief, was then taken away for questioning although authorities have not confirmed if he has been formally arrested.
Salih has recently received threats from security forces over Aljazeera's political coverage of Sudan.
The channel, whose motto is "The opinion and the counter opinion", has given government and opposition figures a platform when reporting on the country.
Human rights organisations have often condemned Sudan for cracking down on freedom of expression.
In its 2003 report on Sudan, Amnesty International said security forces continued to limit media freedoms.
It added that authorities unlawfully arrested journalists and editors and fined or suspended newspapers.
Sanctions were also imposed for publishing articles critical of the government.