Nkunku, who signed from RB Leipzig in July, needed surgery for a knee injury he suffered in a pre-season friendly, but has recently returned to training and had hoped to be involved after the international break.
"Last week, he took part in a few training sessions, still he's not fully recovered to be part of the tactical sessions," Pochettino said.
"Really bad luck to lose him for the beginning of the season. Step by step we will find the best way for him to fit in the team."
Romeo Lavia (19) is another player yet to make his debut for Chelsea since his signing, the Belgian midfielder is out with an ankle injury, and Pochettino said he was a little behind Nkunku but in good condition.
Chelsea struggled early in the season, with just one win in their opening six league games, but go into Saturday's game with Newcastle on the back of a 4-1 win away to Tottenham Hotspur and a 4-4 draw with Manchester City.
"We were not consistent in the first period of the competition. We talked today in our meeting to try to find why," the manager said.
"We were very good against Arsenal, Liverpool and struggled against teams with less quality than us and play in a different way.
"We need to be consistent in the way we think. It's important to assess after a period, when you win the perception is different.
"Most important is we are more confident and tomorrow we need to confirm we are in a different way."
Chelsea are 10th in the Premier League on 16 points, and travel to face a Newcastle side four points ahead in seventh.
