Messi was banned and fined $50,000 by CONMEBOL in August for accusing the governing body of corruption in the wake of Argentina's Copa America semi-final defeat to hosts Brazil.
The Barca talisman has missed Argentina's past four matches – all friendlies – as a result, but he was named in their latest squad on Thursday for upcoming matches against Brazil and Uruguay.
Those games will be played this month in Saudi Arabia and Israel, respectively.
Messi has suffered with injury problems this term, leading to some suggesting his return to the Argentina set-up could be a negative development for Barcelona.
Although Valverde's tone seemed to a suggest a hint of frustration, he refused to outright call Messi's call-up a problem.
"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."
Defender Samuel Umtiti has endured a wretched time with injuries over the past 18 months, playing just 15 LaLiga matches since the start of last season.
His solitary outing this term against Eibar last month was followed by another knee injury, though Valverde hinted he could potentially feature at Levante on Saturday.
"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."