Urging the 47-state body to send a team of "independent and universally respected experts," Annan said the council must show Darfur's people that "their cries for help are being heard" because the situation there was worsening.
"It is essential that the Council [issue] a clear and united message ... that the current situation is simply unacceptable," said Annan, who steps down as secretary-general at the end of 2006.
Khartoum says Darfur, where long-simmering ethnic violence erupted into war in 2003, has improved since a peace treaty earlier this year with one leading rebel group.
It disputes the death toll in the region, where over 2 million have been driven from their homes, and pins the blame for violations on rebel groups that are still fighting.
Farah Mustafa, Sudan's representative at the council session, accused Western media of distorting the picture.
He said: "It has been repeating lies, day after day."
Aid workers have said that not even the most basic food or relief is reaching many thousands of people in Darfur despite the world's biggest humanitarian effort. The spiraling violence is forcing many aid workers to pull out.
Kenro Oshidari, the Sudan director for the World Food Programme (WFP), said that about 200 WFP trucks are currently being blocked from reaching Darfur by the government, apparently for bureaucratic reasons or because of worries of violence.
He said: "Food security is one of the most basic human rights, and it's constantly being challenged in Darfur."
Seventy-four WFP vehicles have been attacked and one driver killed since a peace treaty was signed in May between Khartoum and one of the Darfur rebel factions. Violence has only increased since the deal, which other rebels rejected.
Three water engineers working with the UN Children's Fund were killed in June by refugees who thought they came to poison a well rather than fix it. Nine others were abducted in October and five are still being held, said Edward Carwardine, a Unicef spokesman.
He said: "Security is our most serious impediment throughout Darfur."
Over a dozen aid workers have been killed in recent months.
Violence against women
Growing numbers of Darfur women and girls are being raped, mainly by Sudan's forces and allied militias who use sexual violence as a weapon of war with total impunity, human rights activists said on Tuesday.
Victims, who often lack access to medical care and counselling, can be further humiliated under Sudanese law which allows them to be charged with adultery or defamation if they fail to prove rape, they said.
Osman Hummaida, the director of the Sudanese Organisation against Torture, said: "We are particularly alarmed by the widespread recourse to rape and other forms of sexual violence as a means of warfare in Darfur, a phenomenon which has been systematically intensified in the last few weeks."
He cited "daily reports" from camps holding people who have fled violence where women who venture out to gather firewood or water are "abducted, assaulted and raped". Rapes are committed by all parties including rebel groups, he said.
Jane Lindrio Alao, a social worker based in Nyala, South Darfur who has counselled rape victims since 2004, said: "Women and children are in need of urgent protection in the three regions of Darfur. We have a whole traumatised community."