AU spokesman Noureddine Mezni told AFP on Sunday that some of the hostages were released later the same day, but he could not give a figure.
"According to our information, the released persons are currently headed on foot to an AU base in the Tina region," said the spokesman, adding that only when they arrive would it be possible to clarify the number.
"Confusion remains concerning the number of hostages," said Mezni. "We talked before 18 hostages, but the number appears to be higher, as the hostage-takers apparently then took some of the rescuers hostage."
About 40 people were apparently taken hostage, he said.
The abductions took place near the town of Tine on Sudan's frontier with Chad.
The kidnappers were thought to be members of a dissident faction of Darfur's rebel Justice and Equality Movement (JEM), Mezni said.
Saturday's clashes caused the
first AU casualties in Darfur
But the head of the JEM's negotiating team at peace talks in the Nigerian capital, Abuja, said that the insurgent leader they think to be behind the kidnapping had been drummed out of the movement.
"Mohammed Saleh is not a member of JEM. We kicked him out almost six months ago, and right now he's across the border in a neighbouring country," Mohammed Tugod said, apparently referring to Chad but declining to do so explicitly.
"I think this act has been done by Mohammed Saleh, and now we are trying to investigate and find out where he has gone with these people," he said.
Chad, which had 10 soldiers among those kidnapped, condemned the kidnapping as an "indefensible and barbaric act", and its foreign minister called for the immediate release of the hostages.
Blame for clashes
The pan-African body separately blamed the Sudan Liberation Army (SLA), the armed wing of the rebel Sudan Liberation Movement (SLM), for Saturday's deadly clashes near Menawasha on the Khor Abeche road in South Darfur state.
"All the evidence shows SLA direct responsibility for the incident," the mission charged in a statement.
In a statement released in Addis Ababa, the AU said Commission Chairman Alpha Omar Konare "unreservedly condemns the killings and holds the SLA responsible for this wicked and atrocious act".
The abductions took place in a
town on the Sudan-Chad border
"He also demands the immediate release of all abducted AMIS (AU Mission in Sudan) personnel," added the statement.
Mezni said a third soldier died on Sunday of his injuries, increasing the death toll from two military personnel killed on Saturday, on top of the two contractors.
Three other troops were wounded, and two are still missing. All the soldiers are Nigerians.
It was the first time the AU has suffered fatalities in the conflict-torn Sudanese region, where it has some 6300 troops monitoring a fragile ceasefire between black African rebels and government-backed Arab fighters.
It is looking to increase its contingent to 7700.
The latest killings occurred as the warring parties entered a new round of peace talks in Abuja on 15 September.
"This escalation of violence is major source of concern at a time when the Abuja peace talks are facing hurdles," said Mezni.