John Granville, a 33-year-old officer with the U.S. Agency for International Development, was shot and killed while returning home from New Year's celebrations in a diplomatic vehicle shortly after midnight on Tuesday.
His driver Abdelrahman Abbas Rahama, 39, was also killed.
"Right now they haven't pinpointed a suspect but I believe they are very close to that stage," ministry spokesman Ali al-Sadig told Reuters.
A group calling itself Ansar al-Tawhid in Sudan (Companions of Monotheism) later posted a message on a militant website claiming responsibility for the murders.
But al-Sadig played down the claim. "It is not being ignored. But it is not being taken too seriously. The claim should be treated with caution," he said.
Sudan's state media agency SUNA also quoted "authorised sources" as saying that similar online claims had proved false in the past.
"The investigations have made considerable progress in revealing some important lines that could lead to the apprehension of the perpetrators," the sources were quoted as saying.
Agents from the FBI and the U.S. State Department's Bureau of Diplomatic Security flew into Sudan after the attack to work with Sudanese investigators.
Foreign embassies in Khartoum urged their citizens to be vigilant after the attack, a rare occurrence in a capital widely seen as one of the safest in Africa.
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