"If people are disappointed this could be expressed in many ways and one of them could be in a violent way and then... we will go back to square one," he warned.
On January 1, the current African Union force in the war-torn region will merge with the new mission called Unamid to provide almost all of the 6,500 soldiers available.
"You realise how Herculean a task we are now facing"
General Martin Luther Agwai, joint force commander
On Saturday Agwai warned the UN that even at full strength, the mission would be daunting.
"You realise how Herculean a task we are now facing,'' he said.
"If those agreements are not reached, the force will have great difficulties deploying successfully."
At least 200,000 people have already died and 2.5 million others forced to flee their homes in four years of fighting between the Sudanese government and local rebels.
Last week Jean-Marie Guehenno, the UN peacekeeping chief, said the deployment was in doubt following Khartoum's demand for stringent restrictions on the force.
|Only a quarter of the 26,000-strong joint force|
initially promised is ready to be deployed [EPA]
UN officials have blamed Sudan's foot-dragging for much of the delays, saying the government is holding up key equipment at customs and has yet to agree to a "status of operations" for Unamid peacekeepers.
John Holmes, the UN undersecretary general for humanitarian affairs, told The Associated Press the disparity was "very hard to explain" and "we will make the best of a difficult situation".
Holmes on Saturday met governors from northern and southern Darfur with the aim of improving relations between UN aid workers and Sudanese authorities.
"We had very frank exchanges," he said. "We had to agree to disagree on issues such as security, lack of access and forced returns."
More than $1bn is given annually to alleviate suffering in Darfur, but the international community has been reluctant to send troops or costly equipment to protect civilians and aid workers.