Sudanese spy chief Abu Bakr Mustafa has stepped down two days after a revolt in the capital Khartoum, the sovereign council said, adding that the request is under consideration.
At least five people died on Tuesday following a botched mutiny believed to have been waged by members of the spy agency, state media said.
Military officers jointly with government-friendly militia foiled the mutiny that left two soldiers dead and three civilians, authorities said.
The disgruntled National Intelligence Security Service (NISS) is said to have opposed drastic changes being undertaken in the country.
“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 counsel, confirmed.
Abdalla Hamdok, the Prime Minister of the transitional government, however, said the resignation has since been accepted for the "sake of stability".
After consultation with Lt. Gen Burhan, Hamdok tweeted, they have settled on Gen. Jamal Abdelmajeed as the new intelligence boss.
"In search of stability for Sudan, and after discussions with Lt. Gen Burhan, I am glad to announce our joint decision to accept the resignation of Gen Abu-Bakr," he said.
The Prime Minister, who took over after ouster of Omar Al-Bashir, added that "we have appointed Gen Jamal Abdelmajeed instead."
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.
Preliminary reports indicate that the mutiny was waged by officers close to the deposed Sudanese leader Al-Bashir, who is currently in jail.
There was no immediate evidence however, linking the embattled leader to the latest in security concern in the North African nation.