The 31-year-old suffered a groin injury while on international duty with Argentina last week on what was his first return to the international stage since the 2018 World Cup.
He played the full 90 minutes of La Albiceleste's 3-1 defeat to Venezuela but was forced to miss the 1-0 win over Morroco on Tuesday and returned to the Camp Nou to start his recovery.
Valverde has, however, revealed that the five-time Ballon d'Or winner has struggled with fitness issues since the turn of the year, which has forced the club to implement a careful injury management programme to maximise his time on the pitch.
"We think it's OK but he has been coping with these issues for a long time," he told a press conference.
"We were taking care of it before Christmas. We have tried to make the pain subside and we will continue doing it. Now he has had a few days of rest.
"We do everything naturally, we talk to him after suffering a little problem in training and we do everything together. We make decisions together and talk to him to see how he is like I do with others."
Despite his persistent injury woes, Messi has been in typically scintillating form for the Blaugrana this season, scoring 39 goals in 36 appearances across all competitions.
Barca are on course for a treble this term, having opened up a 10 point lead at the top of La Liga ahead of Atletico Madrid , while also securing their passage through to the Champions League quarter-finals and a Copa del Rey final.
Valverde continued by trying to play down the hype surrounding his team's potential achievements come May, insisting that "nothing is won yet".
"The environment escapes me, we have not won anything yet," he added. "Every time they tell me about the treble and the double. What we're not going to deny is that people get excited about the team.
"We are in three competitions and I imagine that people will celebrate the options we have, but we have not won anything".
The Spanish coach also gave a quick update on Ousmane Dembele's recovery from a hamstring injury, stating: "He is doing well and we're confident but I cannot give exact dates. We are within the deadlines set but we will try not to force him".