The UN did not confirm the report, and Negroponte, who concluded a trip to Sudan on Monday, declined to comment on it.
The agency did not give further details about the agreement, which it said was brokered in Riyadh during the Arab summit held in the Saudi capital late in March.
The UN has been nearing a deal with Khartoum to add 3,000 UN military personnel and equipment to the AU force, including fielding six attack helicopters, but Sudan has so far objected to the so-called "heavy support package".
Lam Akol, Sudan's foreign minister, said on Sunday that Khartoum was inclined to allow the helicopters to be deployed and would accept as many AU troops as was needed to stabilise Darfur, but said Sudan would not bow to international pressure to accept a UN force.
Negroponte has pressed Sudanese officials to accept thousands of UN peacekeepers to support what is the world's largest humanitarian effort.
"We must move quickly to a larger, hybrid United Nations-African Union peacekeeping force with a single, unified chain of command that conforms to UN standards and practices," Negroponte told reporters, as he wrapped up a visit to Sudan.
Sudan's government criticised
"The government of Sudan must disarm the Janjawid, the Arab militias that we all know could not exist without the Sudanese government's active support"
US deputy secretary of state
He also said that the Janjawid forces, that are accused of atrocities in Darfur, are supported by the Sudanese government.
His remarks contradict the Sudanese government, which has always denied backing the Janjawid, despite accusations by the UN and the AU.
"The government of Sudan must disarm the Janjawid, the Arab militias that we all know could not exist without the Sudanese government's active support," Negroponte said.
He also criticised Sudan's government saying its record on allowing relief workers access to Darfur was "not encouraging".
"The denial of visas, the harassment of aid workers and other measures create the impression that the government is engaged in a deliberate campaign of intimidation," he said.
Negroponte's visit comes after the US held off on a decision to impose unilateral sanctions against Sudan, in the hope that Ban Ki-moon, the UN secretary general, will be able to convince Khartoum to allow UN peacekeepers into Darfur.
Ban was expected to meet Alpha Oumar Konare, the AU chief executive, on Monday and Tuesday in New York, as well as Jan Eliasson, of the UN and Salim Ahmed Salim, of the AU, both envoys for a Darfur peace accord.