Reports of increasing tensions between the Argentina star and the Barca coach have raised questions over whether Messi will be at Camp Nou next season.
Messi appeared to fuel the fire when he admitted "I don't know where I'll be next year" at Monday's FIFA Ballon d'Or awards.
But Luis Enrique rubbished the idea of Messi plying his trade elsewhere any time soon.
"We all think Leo is going to be at Barca for many years," he said. "That is what we all want as Barca fans. We are not thinking about him not being in the team next season.
"The thought of having a team without Messi is not even something we contemplate.
"We shy away from controversy, comments and rumours. We seek the best atmosphere in the dressing room."
Luis Enrique was also questioned on the improved performances of close-season signing Luis Suarez in recent weeks.
After finding the net just once in his first eight appearances, the Uruguay international has scored in four of his last six - including the second in Sunday's 3-1 win over La Liga champions Atletico Madrid.
And Luis Enrique believes the former Liverpool forward will only continue to get better.
"Physically he is in great shape," the 44-year-old added. "In footballing terms he is continuing to develop.
"As games go by we will see that development and I am sure he will offer great things to the team."
Barcelona travel to Elche for Thursday's Copa del Rey second-leg last-16 clash, a tie the Catalan side lead 5-0 from last week's first encounter.
