The London-based human rights group and rebels in the Darfur region say Khartoum is using the Janjawid, a horse or camel-mounted militia, as a proxy force to crush the revolt.
Fighting erupted in Darfur a year ago with rebels accusing the government of oppressing black Africans and favouring Arabs in an impoverished region historically prone to tensions between the two communities over water and grazing.
"There is clear evidence of cooperation between government forces and government-aligned militia," Amnesty said on Tuesday.
Government officials were not immediately available for comment in Khartoum, where Tuesday was a public holiday.
Relentless government bombing and Janjawid attacks have driven tens of thousands of refugees into neighbouring Chad since December when ceasefire talks collapsed, clearing the way for an escalation in fighting.
"Civilians have become hostages to the situation in Darfur," Amnesty said, adding whole villages were being destroyed to forcibly displace the local population.
Amnesty said Khartoum had largely failed to condemn the killings, maiming, torture, abductions and arbitrary arrests in Darfur.
A revolt erupted in the western
region of Darfur a year ago
"The silence of the authorities regarding the atrocities committed by the Janjawid suggests that their actions are condoned, if not encouraged, by the government," Amnesty said.
According to a witness account in a 43-page Amnesty report, Janjawid militiamen attacked civilians telling them: "You are opponents to the regime, we must crush you.
"As you are black, you are like slaves. The government is on our side. The government plane is on our side, it gives us ammunitions and food."
The United Nations refugee agency said on Tuesday it had registered more than 4300 Sudanese refugees in and around the town of Tine, Chad, which was bombed a few days ago, and hoped to start relocating them this week.
Chadian town of Tine lies deserted
after it was bombed last week
In addition, the office of the UN High Commissioner for Refugees (UNHCR) said it would increase its presence on the ground to deal with the thousands of refugees who had poured into the country to escape violence in the west of neighbouring Sudan.
Meanwhile, the Sudanese government has welcomed Chadian President Idris Deby's decision to renew mediation for a peaceful settlement between Khartoum and rebels in western Sudan, a newspaper said on Tuesday.
North Darfur Governor Usman Yusuf Kabir was quoted by independent Akhbar al-Yum daily as saying he was notified of the new mediation attempt by his Chadian counterpart, the governor of Chad's eastern Wadi Ferra State, at a meeting in Tine last Saturday.
Kabir said he discussed with the governor the conditions of the 100,000 refugees who crossed the border into Chad, fleeing the fighting in Darfur.