City completed the signing of Portugal midfielder Matheus Nunes from Wolverhampton Wanderers on a five-year contract early on Friday, but the 25-year-old was not scheduled to train, casting doubt on whether he would be available.
"I know that he is going to be a City player, but if he's going to be available, I still don't know, we don't have that information," said Lillo, who is filling in for Pep Guardiola while he recovers from back surgery.
City have picked up where they left off last season, winning all three games to top the Premier League table, despite missing Akanji in their 2-1 win at Sheffield United on Sunday with a minor issue.
Foden was on the bench with an illness but played the final few minutes, and assisted Rodri's winning goal.
"Phil is completely recovered from his illness, Manu's problem was more for prevention rather than anything serious," said Lillo, who added John Stones is also nearing a return.
Speculation also swirled around the immediate future of Joao Cancelo, and Lillo was asked if the Portuguese defender would still be wearing City's sky blue come Saturday.
"You can ask me but I can't give an answer," he told reporters on Friday.
"I have nothing to add, I've been in training. I have nothing I can help you with the question."
City have lost midfielder Cole Palmer after he completed a surprise move to Chelsea.
"It's very difficult to go against a player's wishes," Lillo said.
"When a player wants to go, it is very difficult to go against that. We have to work out the operation that has value for the club as well. On the other side, there is a pride that a young player (will be) starting to give life to the rest of the country, like at Chelsea.
"We have to be proud and satisfied at Manchester City that we have done this. To deny a footballer the opportunity to do what he wants to do is very difficult."
It is uncertain when Guardiola will be back running the show in person, but Lillo said the manager is still very much involved.
"I speak very regularly with him, not just in footballing terms but professional terms," Lillo said.
"He's much better and things are taking place the way that they should do. All of us are delighted and are really looking forward to him getting back."
