Messi – making his first LaLiga start of the season following a calf injury – was withdrawn at half-time of Tuesday's 2-1 victory over visiting Villarreal.
The Barca captain pulled up and walked off the pitch for treatment with what appeared to be a thigh problem at Camp Nou.
Messi eventually returned to complete the remainder of the first half, however, the 32-year-old did not emerge for the second 45 minutes as he was replaced by Ousmane Dembele.
"He had some discomfort in the adductor and we decided not to keep him on as a precaution, but we have to wait until tomorrow [Wednesday to find out more]," said Valverde.
Asked if the issue could be down to a lack of time on the training pitch before his return, Valverde added: "It's a handicap for him, for Luis [Suarez] and Dembele.
"In the end, it's early in the season and you need games to find a rhythm. But that's hard because the teams are in shape."
Messi, who claimed the Best FIFA Men's Player award in Milan on Monday, was making his 400th LaLiga appearance for Barca.
He was instrumental in Barca's opening goal, supplying the cross for team-mate Antoine Griezmann to head home in the sixth minute.
Arthur blasted in the stunning second nine minutes later, with Villarreal unable to find an equaliser after Santi Cazorla's swerving effort fooled Marc-Andre ter Stegen on the stroke of half-time.
"[Messi] had discomfort," Griezmann told Movistar after the match. "I don't know what else because we haven't had time to talk to him because the coach gave tactical instructions."
LaLiga champions Barca are back in action against Getafe on Saturday.