Messi began Barca's 1-0 defeat to Real Sociedad on Sunday on the bench - heightening talk of a fall-out between player and manager.
Recent reports in the Spanish media have suggested Messi is unsettled at Camp Nou due to the row with Luis Enrique, with those rumours fuelled by his absence from training on Monday.
While Barca stated this was down to a bout of gastroenteritis, Luis Enrique was forced to field a raft of questions over the superstar forward in his news conference on Wednesday.
Despite the speculation and departure of director of football Andoni Zubizarreta on Monday, the Barca coach said he retains support in both the dressing room and board room.
"Things always depend on results, that's the first thing when you take over as manager. You need results but I feel supported by the club and the players," he said.
"I have no doubts in that respect. I have nothing to feel sorry about regarding my personal relationship with my players. Managers need to deal with their squad that's what I'm doing.
"We're judged on what happens at the end of the season and that's what we're working towards. I feel confident, I feel motivated thinking about the things we can improve and the things we can control."
The situation with Messi has led to reports of a move away for the four-time Ballon d'Or winner, but Luis Enrique refused to deal with further speculation.
"I think I've said it before, he's important. He's the greatest player in the world, generally that's agreed," the former Celta Vigo boss added.
"If he's best in world then he is also the best player in my squad. I've said it enough times, it doesn't make sense repeating myself.
"At the minute it's all so negative in a wide variety of forms. I shouldn't be asked to confirm or deny different rumours. That would stir up more problems that it would solve.
"I'm sailing the Barca ship, I try to keep away from rumours because there are such a wide variety. I can't confirm or deny these rumours that appear.
"I'm going to keep doing my job as well as I can for the benefit of the team. I'm here to serve the club. That's what I intend to do while I'm here."
