The 32-year-old was banned and fined $50,000 by CONMEBOL in August for accusing the South American football governing body of corruption following Argentina's Copa America semi-final defeat to Brazil.
Messi is in contention to play in Argentina’s upcoming games against Brazil and Uruguay after Lionel Scaloni included the Barcelona captain in his 26-man squad.
The Argentine missed the start of the season through injury and many suggested that he should have been rested during the international break.
Valverde was speaking to the media ahead of the La Liga champions’ visit to Levante on Saturday and he said he does not think Messi returning to international duty is a setback to the Blaugrana.
"Look, we know that if Messi is active, there's a good chance he gets called up to the national team," Valverde told reporters on Friday.
"He hasn't been [in the Argentina squad] because of suspension, but now that's over it's normal for him to be back for Argentina.
"It's something we accept, he accepts. I don't think it's a setback as such."
Valverde updated the media about the availability of Samuel Umtiti, a player who has been troubled with injuries since the start of last season.
"Let's see how he does in training today [Friday]," Valverde said. "He's had fitness issues hanging over from last year, that's why he's not playing regularly.”
"Hopefully we can get this sorted once and for all so he can play more regularly, but the other thing is competition for places. Lenglet is playing very well.
"He [Lenglet] is an absolutely reliable player, very professional in what he does. He's really settling into his position.
"Shortly after arriving last season, he covered extremely well for Samuel and the French team is also aware of how well he is playing."
