Barcelona's injury woes continue as midfielder Fermin Lopez was dealt a blow with a new muscular issue in his right thigh during training on Tuesday.
The Catalans were already without new signing Dani Olmo, who is sidelined for up to five weeks with a right hamstring injury, and fellow midfielders Gavi, Frenkie de Jong and Marc Bernal, as well as defenders Ronald Araujo and Andreas Christensen.
"When we started the season, I said there would be no excuses," Flick told reporters ahead of Sunday's fixture. "We're going to be able to manage the game, although we'll be careful with some players carrying a lot of load.
"Tomorrow we'll manage this, although I'm sure that those who come on will be at 100%. The medical team is helping us and we are taking special care with (Pau) Cubarsi, who has been recovering."
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Barcelona have made a perfect start to the LaLiga season under the German, with five straight wins putting them top of the standings, four points ahead of defending champions Real Madrid.
Villarreal are fourth in the table with three wins and two draws in five matches.
"We have a great team, and we have shown it," Flick said. "Every season it's the same, there are weeks when you lose several players, but as a coach, it's something you have to accept.
"Now we have to focus on those who are available to prepare them for the next game."
Barcelona's only defeat so far this campaign came in their Champions League opener to Ligue 1 club AS Monaco, where they lost 2-1.
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