"For the first time, I visited them [rebels] in the field in Um Rai [North Darfur] ... and I was able to get a ceasefire commitment from them," Aprezi said.
"Unfortunately [Sudan's army] went and bombed the area and it looks like I led them to the area to get bombed."
The meeting was held on Friday and he notified the government of it, he said.
Aprezi's AU force, hampered by lack of equipment and funds, has struggled to stem the violence in remote western Sudan.
A peace deal was signed between one of three negotiating rebel factions and the government in May.
Rival rebel groups rejected it, formed a new military alliance and renewed hostilities with the government.
A government army spokesman said there was no confirmation of this in Khartoum.
"Darfur commanders cannot undertake bombing operations without the knowledge of central command in Khartoum," the spokesman told Reuters news agency.
"But we in central command are completely committed to the ceasefire."
Following the new bombings, it was unclear if rebel groups would honour the ceasefire negotiated by Aprezi on Friday.
The fighting has driven 2.5 million people from their homes and killed an estimated 200,000.