There have been widespread reports that Luis Enrique's relationship with Messi is beyond repair following a falling out between the two men last month.
Barca defender Jeremy Mathieu revealed details of the training ground bust-up at the time, though he played down the incident.
Pique has now done the same, while insisting Luis Enrique has full control of the dressing room in wake of rumours suggesting Messi is allowed to do whatever he wants in Barcelona.
"Luis Enrique calls the shots more than Messi, obviously," Pique told Spanish radio programme El Partido de las 12.
"He's the coach, the boss, though Leo has a lot of clout in the dressing room. There are disagreements in every squad.
"Luis Enrique and Messi had a spat, but it's a thing of the past."
Pique also spoke about his own future at Barca, revealing that he wants to retire at his boyhood club.
"I love this profession more and more each day and I'd like to keep on playing," said the 28-year-old.
"I can safely say that I plan to retire here at Barca, whether that's at the end of this season or six years from now. I won't play for another club."
