Government officials said on Friday that the document drafted by African Union mediators was too one-sided.
"Still we are negotiating and consulting. The headache concerns the prohibition of flights over Darfur. The issue of the Janjawid is also being discussed," government spokesman Ibrahim Muhammad said.
But the mediators said they hoped for agreement in the Nigerian capital Abuja by the weekend now that the rebel side has agreed to sign the plan after two weeks of talks.
The slow-moving talks aimed at ending the Darfur conflict, which has driven 1.5 million civilians from their homes, have been plagued by accusations of ceasefire violations on both sides and deteriorating security on the ground.
"Still we are negotiating and consulting. The headache concerns the prohibition of flights
over Darfur. The issue
of the Janjawid is also
The draft security agreement drawn up by mediators calls for a military no-fly zone over Darfur and the disarmament of the pro-Khartoum militias known as Janjawid.
The plan does not contain Khartoum's demand that the rebels must move their forces into barracks. Instead it asks the rebels to give information on the whereabouts of their forces.
A rebel negotiator said: "This protocol won't guarantee full security in Darfur, but it will be the first step."
Fighting began in the arid Darfur region in February 2003 after years of low-level fighting between farmers and nomads over scarce resources.
The rebels accuse Khartoum of neglecting Darfur and using Janjawid militias to loot and burn villages. Khartoum denies the charges.
There are no reliable estimates of how many have been killed in the violence, which the United States has called genocide. But the UN has said 70,000 people have died from disease and malnutrition since March, a figure disputed by Khartoum.
Previous Security Council resolutions have threatened sanctions, including possible measures targeting Sudan's oil industry, if the government failed to meet commitments to end attacks on civilians and rein in the militias.
The Security Council plans to hold a meeting on 18-19 November in Nairobi to discuss Darfur.