The 22-year-old has been told he can return to his native Tiwi Islands this week to deal with the continuing stress associated with the death of his father Matthew in November, and his mentor Maurice Rioli on Christmas Day.
Bailey said Wonaeamirri had become "disconnected from his culture and his people", and would use this time to "regroup" after trying valiantly to fight through his issues over the past few months.
"It's disappointing but we're also very understanding. You've got to understand there are 46 players at each club and they all face different traumas or challenges during their life," Bailey said on Tuesday.
"His is a little bit different however, the trauma that he's gone through has been fairly significant.
"Obviously his father and his culture is very important to him and this is his opportunity to go back and reconnect."
Bailey revealed Wonaeamirri had spent a week at his house in the lead up to the decision made to allow him to go home.
He said he had gotten to know the 31-game player well and gained an insight into how hard he had tried to fight through his problems.
"We went for three or four walks in the evening and he was really working hard to stay and play as a Melbourne footballer," Bailey said.
"He's just got to a stage now where he feels like he needs to go home so there's a little bit of homesickness about it as well.
"Part of being a coach is trying to help players through some difficult times in their lives, and I spoke with Aus about coming and spending a week at my place.
"He got to know my kids well and the players were taking the mickey out of him, to be honest, you know, 'You're at home with the coach so things are looking good for you'.
"He's just a very likeable young man and everyone would love to see him back playing for Melbourne as soon as he can."
Wonaeamirri has not played senior football since round eight and has managed just five games this year owing to a delayed pre-season after the passing of his father and Rioli.
He missed round nine with a knee injury after stringing together consecutive games across Melbourne's round five bye but returned for the Casey Scorpions in the VFL on the weekend.
Wonaeamirri has been working with Bailey and club personal development coach Ian Flack in recent times and the decision to grant the indefinite leave was jointly reached.
Bailey said the club would continue to support Wonaeamirri throughout this period and were confident he would look after himself and train while he was at home.
"People want the best for him. He's an energetic player and he just brings something special to the game," he said.
"These issues have been there for awhile and now the best thing is to go back.
"We've always been discussing a lot of issues with Aus, this being one of that … we just felt that now he couldn't commit totally to the club at the moment and I'm sure he'll be back better than ever."
Matthew Wonaeamirri passed away at the age of 63 as the result of a car accident in late November, while Rioli, 53, died of a suspected heart attack in Darwin on December 25 last year.
