The Argentina international informed Barca that he wanted to leave the club this summer before ultimately reversing the decision, and he will will now stay at Camp Nou until at least the end of the 2020-21 season.
When questioned on his relationship with the 33-year-old, Koeman insisted that the issue "was mainly a conflict between Messi and the club", implying that there is no problem between the two individuals.
"That has passed me reasonably well," Koeman told Fox Sports. "That was mainly a conflict between Messi and the club. I have spoken to Messi since then and we will continue as usual."
Barca relinquished control of the La Liga title to Real Madrid last season, while they were knocked out of the Champions League at the quarter-final stage by Bayern Munich, suffering an 8-2 defeat.
Messi scored 31 times and registered 26 assists in 44 appearances at club level last term.