Messi, 33, missed Wednesday's semi-final win over Real Sociedad with a thigh injury and only returned to full training on Saturday.
"We will see how he is [after Saturday's session]," Koeman told a news conference ahead of his first final in charge of the Catalan club.
"Messi will have the final say. He knows his body the best. We are hopeful he will be available for the game. You always have a better chance if you have the best player in the world on your team.
"But every player needs to be 100% [fit] to start the game because it's not the last game of the season. We still have many more matches after this one.
"It's about the risk. If he's not ready, someone else will play, and we will play our same game without him."
Barca are unbeaten in nine games in all competitions and Sunday's final against Athletic provides the chance to demonstrate that they've turned a corner following what was a stuttering start to the season.
It also presents an opportunity to win some silverware after last season ended trophy-less for the first time since 2007-08.
"It's important because it's a final and it's a trophy," Koeman added. "To show we're on the right path, it's important to win things.
Barca beat Sociedad on penalties to reach Supercopa final
Marc-Andre ter Stegen makes two big saves in the shootout to help Barcelona top Real Sociedad.
"We know it's not the most important trophy, but it's a trophy. Winning things shows you're on track. One game is not decisive, of course, but it gives you confidence and shows you've improved."
While Barca have got their act together on the pitch in recent weeks, they remain disorganised off it.
The presidential election, originally scheduled for Jan. 24, has been delayed until March due to the coronavirus pandemic, meaning they will be unable to make any signings in January.
"I have heard I am annoyed, unhappy, worried," said Koeman after the three candidates for the presidency -- Joan Laporta, Victor Font and Toni Freixa -- vetoed a move for Manchester City defender Eric Garcia, who will be available for free in the summer.
"But I can say I am fine. I am happy. I know perfectly well the financial limits at the club. And if it's not possible to sign, it's not possible. We continue with what we have."
However, players may still leave Camp Nou this month. Carles Alena has left on loan for Getafe and Koeman's encouraged some of the club's other youngsters to go out and get experience, although he says he wants backup goalkeeper Neto to stay.
"It's true Neto's agent has asked to leave but we have said no," Koeman explained. "We want to be well covered in every position."