Brown will leave for Japan next week to help coach the national side, forcing him to not be the head coach for the Highlanders in the upcoming Super Rugby transtasman competition.
Brown was the Highlanders head coach and is also the Japan assistant coach.
Japan is due to play the British and Irish Lions in Edinburgh late next month and Brown is needed to help with preparation and get the Cherry Blossoms up to speed after 18 months of not playing.
"It was very unfortunate but also exciting at the same time — trying to get Japan rugby back into playing test rugby," he said.
"Having not played for well over a year, almost two years, and playing the Lions in Scotland is a huge challenge for Japan rugby.
"I’m pretty lucky as a rugby coach. Japan let me coach the Highlanders and the Highlanders let me coach Japan. And sometimes it is going to overlap, so it is just unfortunate the way it has worked out.
"I have put myself in this situation as I want to coach both teams. I will be trying my best to make sure both teams win."
Brown said he had good conversations with Highlanders chief executive Roger Clark and understood the situation.
Brown will fly to Japan in the middle of next week where he will then enter two weeks of isolation. From there he will have two weeks with the team, then fly to Edinburgh for the game on June 26. Japan coach Jamie Joseph will be on the same flight north.
His two weeks in isolation will not be wasted, as Brown will still have an eye on the team back in Dunedin.
"It is going to be different but I will still have a major role in planning for each game, making sure our plans are right on the money on how to win games of rugby.
"And also reviewing games and making sure the teams have the right feedback, heading in the right direction. Obviously Derms [assistant coach Clarke Dermody] is going to be man on the ground here, driving the team forward every day."
"I have 100% confidence in him [Dermody] as a head coach. He has done that with Tasman."
Brown said it was tough to tell the players he was leaving.
"We put a lot of effort into this campaign and it did not go our way the way we wanted it to.
"It was a hard conversation to have with the leaders and a tough one with the players as well. But it is what it is. I will be on my best to make sure we can win every game of rugby. That will be from Japan. The boys will do a good job I’m sure."
Brown said Highlanders No8 Kazuki Himeno will play the game in Edinburgh. He would head to Scotland after the finish of the Super Rugby Trans-Tasman competition.
"The frustrating part about Covid is we have not been able to play any test rugby since the World Cup. But we created a lot of momentum around Japan rugby in that time.
"But it is 18 months now and we have not played a test. It is going to be a huge challenge for us but an exciting one for Japan rugby."
