A spokesman for the Sudanese armed forces said the attack was the result of a "shared mistake".
He said the U.N./AU Mission in Darfur (UNAMID) had failed to warn his soldiers they would be passing through the area, Sudan's state news agency SUNA reported.
"The Western Sudan Military Command has provided an apology to the representative of UNAMID in the region and ... the apology was accepted, in recognition of the dual mistake committed," SUNA added.
Sudanese soldiers fired light weapons and rocket-propelled grenades at the UNAMID supply convoy for up to 12 minutes as it headed for the west Darfur town of Tine late on Monday, the United Nations said.
Officers on the ground told Reuters soon after the attack that they assumed the Sudanese soldiers had mistaken the peacekeepers for rebels, who have been increasingly active in the region in recent weeks.
U.N. peacekeeping chief Jean-Marie Guehenno told the Security Council on Wednesday that the convoy of "clearly marked white vehicles" had been travelling at slow speed when it was hit.
A Sudanese driver was left in a critical condition after being shot seven times.
On Wednesday, Sudan's ambassador to the United Nations, Abdalmahmoud Abdalhaleem, had insisted to journalists that Darfur rebels, not government forces, were behind the attack.
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