"There's some risk that, as you move toward the peace process, that you are going to get these players trying to position themselves over the coming weeks," the high level US official said while visiting the troubled region in western Sudan.
"In a sense, they are trying to position themselves in territory and assets," he added.
Zoellick spoke to reporters a day after he met Sudanese President Omar al-Bashir in Rwanda and pressed him to accept NATO support for peacekeepers to stabilize the area.
AU troops deployed
The US envoy flew to Darfur to visit some of the 2200 African Union (AU) peacekeepers who are trying to calm the desert region, the scene of one of the world's worst humanitarian crises.
"The African Union team is playing a critical leadership role in what we all know is a terrible problem," Zoellick said.
Zoellick commented that the Khartoum government had to stop its allied groups from attacking civilians. "They have the responsibility in the Sudanese territory to disarm the militia," he said.
"The African Union team is playing a critical leadership role in what we all know is a terrible problem"
Robert Zoellick, US Deputy Secretary of State
He said it was hard to say whether the pro-government tribal groups were still receiving instructions from Khartoum.
Support of Nato
"I do believe that the government now believes that it is in [its] interests to try to reach an accommodation with the rebels. I'm saying the eyes of the world are on you," Zoellick said.
Over 2000 Nigerian led AU troops
are deployed in Darfur
In his meeting with President al-Bashir at a regional summit in Rwanda, the envoy said he had encouraged Sudan "to welcome the support of Nato so that it helps bring in more AU troops more quickly and support the logistic side, am happy they have done that."
Asked whether the groups - who belong to at least three tribes - were sufficiently united in their goals to reach a peace settlement, Zoellick said: "It's hard to say. I don't think they're very unified now. I think the process of the talks increased the likelihood that they will be pressed to unify."
Janjawid alleged abuses
The crisis in Darfur erupted when tribal groups took up arms against what they saw as years of state neglect and discrimination against southern Sudanese.
The government is accused of responding with a counterinsurgency campaign in which nomadic militias known as Janjawid committed wide-scale abuses against other anti-government tribes.
According to western human rights groups, at least 180,000 people have died, many from hunger and disease, and about two million others have fled their homes to escape the conflict between rebels on one side and government troops and Arabs on the other.
Major conflict has ended but violence and rape targeting civilians continues to be reported.