"The tweets claimed poor treatment from crew and discrimination on the basis of race. We replied that there appeared to be a misunderstanding on-board that was exacerbated by the fact will.i.am was wearing noise cancelling headphones," the memo reads.
"We rejected claims of racism and have since asked will.i.am for a retraction of that claim. We fully support our crew and the great work they do ensuring safety of all those on-board."
Will.i.am is also copping criticism from a flight attendants association for revealing the identity of the staff member whom he's accused.
He said the incident took place as the crew was preparing to land the flight in Sydney, and it's understood he refused to show his boarding pass and ignored safety directions to stow his laptop.
However, he claims he had not heard announcements over the PA because he was wearing noise-cancelling headphones.
The female flight attendant has been bombarded with abuse on social media from the musician's fans who have labelled Qantas the "white supremacist airline".
Will.i.am's decision to identify her has been criticised by the Flight Attendants Association of Australia secretary Teri O'Toole, who said the crew member is being abused for simply doing her job.
She told The Australian takeoff and landing were "critical operational times", and a flying laptop could cause serious injury to another passenger or crew member.
"These are safety protocols that have been put in place by Qantas," Ms O'Toole said. "As employees, crew are bound to follow their employer's direction. It seems that in doing this, crew are being vilified and attacked on social media."
Facing similar criticism on social media, will.i.am tweeted that if he was the "slightest bit rude to a FAN or a journalist during work" we would expect to be called on Twitter too.
When the plane landed on Saturday, will.i.am was met by five police officers, who let him go without further incident.
"Qantas, your racist flight attendant was beyond rude and took it to the next level by calling the police on me. Thank god the other passengers testified that she was out of control. The police finally let me go. Imagine if the police were as aggressive," he said.
"Is calling the police on a passenger for not hearing the PA due to wearing noise cancelling headphones appropriate?
"I did comply quickly and politely, only to be greeted by police. I think I was targeted."
He went on to allege the flight attendant "singled every person of colour in the flight and gave them a hard time", and that "other passengers on the flight agreed that she was out of hand".
He later defended his actions to the Sunday Telegraph.
"I've never seen this, it was like a police state," will.i.am told the publication.
"I am the coolest traveller, I don't ask for much. I try to stay out of their way. I come on the plane to go to sleep or I go to work.
"I wish no harm to that lady, hopefully this is a lesson," he said.
"She shouldn't lose her job over it — if anything she should be retrained on how to deal with people. This is an opportunity to be pleasant to everyone, to just be nice."
The singer also retweeted a couple of people who said they were on the same flight, and agreed with him.
Meanwhile, Sunday morning brought a twist in the story when Australian band The Veronicas tweeted "in support" of the singer, claiming the same flight attendant was involved in an incident with them as well.
"We feel sickened she was given no reprisal and has instead continued to abuse her position, discriminate and misuse the full force and intimidation of the Australian Federal Police to her agenda," they tweeted.
"Qantas should have run a genuine investigation into the matter instead of shifting blame and denying accountability."
Sisters Lisa and Jess Origliasso made headlines after they were "embarrassingly" removed from a Qantas aircraft by three federal police.
Qantas' celebrity spat in September with The Veronicas kicked off on the same route but travelling in the opposite direction, from Sydney to Brisbane.
It resulted in the plane being stuck on the tarmac for 45 minutes.
There were conflicting accounts from passengers at the time, with some backing the sisters' assertions that Qantas had been unreasonable and others accusing the pair of being "belligerent".
Qantas said they had "refused to follow crew instructions and were offloaded".
