Fowler, 23, this week withdrew from the squad to play world No.3 Germany on Saturday (AEDT) and Haiti on Wednesday.
"It's really important that we create an environment that is important for the player, and as the circumstances are private I'm not going to elaborate," Montemurro said.
"But yes, absolutely, discussions were had with Mary, with the club (Manchester City), and with the relative people, and we believe that we've made the right decision and I think everyone's in support of the situation."
There has been speculation that Fowler has returned to Australia to support her partner, Nathan Cleary, which Football Australia has not confirmed.
The Penrith rugby league star required emergency surgery after suffering a career-threatening badly broken leg in the Panthers' NRL preliminary final loss in late September.
"No, I don't know what the situation is," Australian goalkeeper Mackenzie Arnold said.
"I messaged both her and Nathan when it happened just to say 'I hope you guys are doing OK.'
"But yeah, I'm not really sure the actual reason that she's headed home."
Players opting out of windows for personal reasons is not rare, especially given the intense schedules of club and international football.
"At the end of the day, we're all human. You can't always base your life around football," Arnold said.
"I have never personally been in that experience, so I don't really know how to put it into words.
"But I would say if I had that situation that I felt the need to go home and I asked the coach for that and I had full trust in him that he was going to give me that permission - then of course, it's important.
"But I think the the bottom line is, at the end of the day we're all human, so if we need to make that decision, then that's what we need to go with."
The Matildas are without three of their best creative outlets - Fowler, Kyra Cooney-Cross and Katrina Gorry - for this window.
But Montemurro backed Australia's "very, very talented" midfield depth.
"This is now a great opportunity, a fantastic opportunity first of all, to bring them in and to understand what we're trying to do in terms of from a high-performance scenario, but more importantly now to be able to expose them against some of the best midfielders in the world," he said.
Montemurro name-dropped Vittsjo gun Dani Galic, Nottingham Forest midfielder Alana Murphy and uncapped Valarenga playmaker Hana Lowry.
"They're names I want you to remember, because I really do believe that they're going to be the next generation of midfielders," he said.
"And look, I'm getting goosebumps just thinking about the amount of midfielders, and talented midfielders, that we have in Australia, and I think that that needs to be a starting point for us."
Ranking points are on the line ahead of December's World Cup draw.
A win over Germany would help world No.15 Australia stay firmly in pot two out of four, meaning a mathematically better draw.
"I wouldn't say we really take any game as a friendly," Arnold said.
