Sudan's spy chief Abu Bakr Mustafa has stepped down two days after a revolt in the capital Khartoum.

“The director of intelligence has resigned. He called us by telephone and we asked him to submit a written resignation, so we are now considering it,” General Abdel Fattah al-Burhan, the head of Sudan's sovereign council, told state television on Wednesday.

The revolt on Tuesday, involving former spies linked to former president Omar al-Bashir and armed forces over severance payout, left two people dead and four others injured.

Gen Burhan added that a committee had been formed to investigate the people behind the confrontation.

Mustafa was appointed the head of the powerful General Intelligence Service, formerly National Intelligence and Security Service (NISS), shortly after the resignation of Salah Gosh in April last year.

Normalcy has been restored in the capital with residents demanding a relocation of military bases operated by the intelligence agency in Khartoum.

Meanwhile, the Sudanese Professionals Association, an umbrella of several trade unions, has said Tuesday's riot was an attempt to drag the country into the circle of violence.

"We call all people to raise the level of organisation and willingness to confront all the scenarios that seek to back down from the people's dues for which the blood of the martyrs and the precious sacrifices were made," SPA said in a statement.