"In the past two weeks we've been limited in what we could say about Australian mum Sally Faulkner and our crew detained in Beirut," Usher said.
"Now they're back we can start to address this complex and distressing chain of events.
"There's one thing we want to state very clearly from the outset: We made mistakes."
Amid an internal review of the story, Usher said that "a lot of soul searching" was underway at Channel Nine. He called the story "a failure which ended very badly for everyone involved".
But for Tara Brown, there appeared to be no question about whether the team should have pursued the story.
Asked when she realised that the situation was dire, she said: "I thought when we presented ourselves [in court] and were being questioned, I really thought: 'We're journalists, we're doing our jobs'- they will see reason, they'll understand that, you know, that we are here just to do a story on a very, very desperate mother. And I just thought that reason would prevail, and it didn't."
A tearful reunion between Ms Faulkner and her mother Karen, new partner Brendan, brother Simon and new baby Eli, showed the sobering reality now facing the family.
Brown appeared flushed when her colleague suggested Ms Faulker was now in a worse position than before embarking on the story.
"I've spent two weeks with Sally, on and off, in cells," she said.
"She's lost everything, she's lost her babies, and I've been completely in awe of how she's coped with that."
But, she said, Ms Faulkner believed she had done what she had to do.
"Despite how terribly it's gone, she knows in her heart that she's tried everything to get them back," Brown said.
"That's in her opinion that she had no choice but to do this, and that ultimately she'll be able to tell them that she tried everything."
Ms Faulker described her tears at having to say goodbye to her children for the last time after agreeing to abandon her custody claim.
In a heartbreaking detail, she recounted how her 6-year-old daughter Lahela gave her a Barbie ring, saying: "This is so you don't forget me."
Embracing her family members, she said: "I had to try."
"We wanted you to try," mum Karen replied.
Channel Nine is expected to reveal more details of its review of the 60 Minutes saga in coming weeks.