Brown is entering the final year of a three-year contract to coach the Otago side and whether he continues in that role should be decided in the next few weeks.
Brown is in his first year as assistant coach with the Highlanders. He is in South Africa and could not be contacted yesterday.
Otago Rugby Football Union general manager Richard Kinley said yesterday the union was waiting to see what was happening with Brown and the Highlanders, and that would affect whether Brown would continue with Otago.
Under New Zealand Rugby Union rules, coaches employed by the national union cannot coach ITM Cup teams.
The Highlanders have four coaches - head coach Jamie Joseph, and assistant coaches Scott McLeod, Brown and Jon Preston.
Joseph and McLeod are employed by the New Zealand Rugby Union and the Highlanders employ Preston and Brown.
Highlanders general manager Roger Clark earlier said it was not ideal to have a coach involved in both Super rugby and an ITM Cup side, as it was too mentally taxing.
Kinley said Brown's involvement with the Highlanders had benefited Otago.
Brown was a real advocate for Otago players and Kinley said 15 Otago players had been involved with the Highlanders this season, which was a bonus for both the players and Otago rugby.
Brown usually spent up to three or four months in Japan coaching but did not do that this year, as he was working with the Highlanders, so he could watch some club games.
The Otago squad for the ITM Cup is due to be named this Friday and will go into fulltime training next Monday.
It has three warm-up games before its first ITM Cup game against North Harbour at Forsyth Barr Stadium on August 16.