Minutes before his arrest, Salih informed his head office in Qatar that the authorities had decided to close the Aljazeera office. He quoted the Sudanese security forces to this effect.
On Wednesday, the office was were raided by the security forces and Salih taken in for questioning.
Broadcasting equipment was confiscated despite production of legal documents and permits.
Salih had recently received threats from the security forces over Aljazeera's political coverage of Sudan.
The channel, whose motto is "The opinion and the counter opinion", had 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.
Amnesty added that authorities unlawfully arrested journalists and editors and fined or suspended newspapers.
Sanctions were also imposed for publishing articles critical of the government.