Mr Ping urged the UN to suspend its investigation into Mr Bashir
The AU has accused the International Criminal Court of "pouring oil on the fire" by seeking the arrest of Sudan's president for war crimes in Darfur.
Chairman of the AU Commission Jean Ping made the remark after talks with Omar al-Bashir in Sudan's capital, Khartoum.
The AU has made it clear any move to indict President Bashir for genocide could hamper peace efforts in Darfur.
Mr Ping urged the UN Security Council to suspend the investigation into the Sudanese president as soon as possible.
He said it should take into account not only the problem of justice, but also that of peace.
Mr Ping was speaking in Khartoum's presidential palace after meeting Mr Bashir to discuss efforts by the ICC to have him indicted for alleged genocide.
'Oil on the fire'
Mr Ping said the ICC had chosen a bad time to pursue the case against the Sudanese president.
Mr Bashir visited UN peacekeepers in Darfur in July
"While we are trying to extinguish the fire here with our troops, we don't understand very well that they chose that moment to put more oil on the fire by taking the decision," he said.
The decision last month to present the case against the Sudanese president has been welcomed by human rights activists, says the BBC's Amber Henshaw in Khartoum.
But regional leaders fear an indictment would cause problems for the international peacekeeping force and stall any peace talks, our correspondent adds.
During a two-day visit to Sudan, Mr Ping has held talks with Mr Bashir and other senior Sudanese officials on Darfur and the deployment of UN and AU troops to the troubled region of western Sudan.
Most of the 9,500 peacekeepers in Darfur are Africans.
ACCUSATIONS AGAINST BASHIR
Killing members of the Fur, Masalit and Zaghawa ethnic groups
Causing these groups serious bodily or mental harm
Inflicting conditions of life calculated to bring about these groups' physical destruction
Crimes against humanity:
Attacks on civilians in Darfur
Pillaging towns and villages
There should be 26,000 soldiers and police in total, but UN bureaucracy and delaying tactics by the Sudanese government have held up the deployment, our correspondent says.
ICC Chief Prosecutor Luis Moreno-Ocampo sought an arrest warrant against Mr Bashir in July, over his alleged role in Sudan's western Darfur region.
He accused Sudan's leader of running a campaign of genocide that killed 35,000 people outright, at least another 100,000 through a "slow death" and forced 2.5 million to flee their homes in Darfur.
Mr Bashir has said he is not worried by the accusations and his government has denied mobilising the Janjaweed militias, accused of widespread atrocities against Darfur's black African population.
The UN estimates that five years of conflict in Darfur have left 300,000 people dead and more than two million people homeless.