Messi has been recuperating from an adductor muscle injury, while Neymar missed Barca's season-opening win at home to Elche due to an ankle problem and only played the final half-hour of the victory at Villarreal in their second outing.
"Neymar is in optimal condition, like almost all the players," Luis Enrique told a news conference previewing the game at the Nou Camp.
"Messi has been working on the sidelines all week and later on joined his team mates," added the former Barca and Spain midfielder, who took over from Gerardo Martino at the end of last term.
Midfielder Andres Iniesta and defenders Thomas Vermaelen and Jeremy Mathieu have also been struggling with minor niggles but trained on Friday as Barca prepare to meet a strong Bilbao side that Luis Enrique called "the best at pressuring in attack".
Barca are the only team in the Spanish top flight to have won their opening two games as they seek to improve on last season's second-placed finish to Atletico Madrid.
"Pressure and strategy are two of their (Bilbao's) great weapons," the coach added. "We will try to counteract that and the players have been warned.
"They don't hesitate. They go on the attack and dominate many aspects of the game."
Bilbao finished fourth last season and are one of four Spanish teams competing in the latest edition of the Champions League, along with Barca, holders Real Madrid and Atletico.
(Writing by Iain Rogers, editing by Ken Ferris)
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