The Argentine is worried that his Brazilian team-mate will be out of action for a prolonged period after injuring his ankle in Thursday's Copa del Rey win
The 21-year-old fell awkwardly early in the Catalans' 6-0 aggregate victory over the Madrid club and was assisted off the pitch by medical staff, visibly in a lot of pain.
Coach Gerard Martino said afterwards that Neymar "won't be playing for a while", and Messi, who has only just returned from a lengthy spell on the sidelines himself, is hoping that the Selecao star can return to action swiftly.
"What happened to Neymar is a real shame," the 26-year-old told reporters. "Tomorrow there will be more tests.
"We hope it's nothing bad, we need him, he's important for the team."
Neymar's injury woes shifted the limelight away from Messi in Thursday's win, with the Argentine scoring his third and fourth goals of 2014 in the second-leg last-16 encounter - the second of which came after a brilliant solo run.
Messi, however, thinks he is still some way off the pace as he continues his comeback from six weeks out of action.
"I feel good, but I still lack that little extra," he added. "I need some more playing time to catch the rhythm and be at my best."
Barca now have three games with Levante on the horizon - first on Sunday in La Liga, then twice in consecutive midweeks in the Copa del Rey quarter-finals.