However, McKenzie is confident Rogers will stay with the 15-a-side game and fulfil his contract with New South Wales for 2007.
"We had a discussion which I had been seeking to have and it is clear there are some issues in his life," McKenzie said in the Daily Telegraph.
"Mat has gone away to consider some of those and we have agreed to have a chat next Tuesday.
"I'm pretty confident at this stage he is going to be with the Waratahs next year - he has a contract and he is going to be with us."
Rogers made it clear to journalists upon his return to Australia that he thought he didn't get enough time at his preferred position of fly-half on the recent Wallabies tour, and McKenzie alluded to other personal problems in the star back's life that was putting his future in rugby in doubt.
"There are a range of issues away from the game (that Mat is considering) - there are issues in and around sport in general," said McKenzie.
"He has some broader issues in his life - it's not my place to talk about the details here.
"His life hasn't always been simple, it has been complicated by different events and that has had an impact on his career.
"We had a very candid discussion - I think that was more reflective of the relationship we have had."
However, McKenzie stopped short of assuring Rogers the fly-half position in the Waratahs line-up for next season's Super 14 competition.
"I am open-minded. I don't promise positions," McKenzie said.
"It's about the team and what is best for the team. A lot of young guys are also coveting the number 10 position but my job is to coach the squad to play as a team.
"I have to be careful I don't spend my time coaching the team for the benefit of individuals."