Commissioner Terence Cole QC said AWB's failure to produce the documents earlier raised questions about whether other key material had not been handed over for investigation.
He demanded AWB provide a "satisfactory explanation" for the delay.
The documents relate to AWB's dealings with a British-based company, Ronly Holdings.
The inquiry has heard that AWB used Ronly to funnel kickbacks to Saddam Hussein's regime in Iraq via the payment of so-called "trucking fees" to a Jordanian-based transport firm, Alia, which was part-owned by the Iraqi government.
Mr Cole said AWB had handed over more documents to the inquiry last night and three more volumes this morning.
But after he and his legal team examined them, Mr Cole said it was apparent they should have been handed to the inquiry, which began pubic hearings in January, much earlier.
"It seems apparent to me these documents ought to have been produced months ago. I am unable to understand why they were not,” Mr Cole said.
"The concern I have is that I do not know what other documents there are which have not been produced to me."
AWB's barrister James Judd QC said he believed if the documents had been produced earlier they could have helped shorten the lengthy inquiry.
"There is no doubt about the relevance of this document," he said, adding that when it was discovered arrangements were made to deliver it to the inquiry immediately.
Mr Judd said he would ask the former AWB senior executive Jill Gillingham to provide a statutory declaration about how documents had been produced to the inquiry.