Chelsea signed Nkunku from Germany's RB Leipzig for more than 50 million pounds in the close season, but the France international missed the first part of the campaign with a serious knee injury.
Nkunku made his first appearance for Chelsea on December 19th, but picked up what Pochettino had earlier described as a minor hip issue against Luton Town on December 30th and missed Chelsea's 1-0 League Cup defeat at Middlesbrough in midweek.
He was expected to return to the side for Saturday's Premier League home game against Fulham, but Pochettino told a news conference that he was no longer sure when Nkunku would feature again.
"I do worry about the situation of Nkunku," Pochettino said. "I think it's now (been) 10 days that he cannot train. We're assessing him. We don't know what's going to happen.
"It was a small issue and it (got) complicated. We're disappointed because we want him involved again as soon as possible."
There was better news elsewhere in the squad, with defenders Ben Chilwell (27) and Benoit Badiashile (22) and midfielder Carney Chukwuemeka (20) all back in contention for Saturday's match after spending time out injured.
Pochettino said his players were in good spirits despite their demoralising defeat by Middlesbrough in the first leg of their League Cup semi-final and that his young squad had the strength of character to take the criticism coming their way on the chin.
"I saw the players today and they were in really good spirits," he said. "Of course they are disappointed with the last game but that was the first 90 minutes. In 10 or 12 days, we are going to play the second leg.
"Sometimes we can learn from being criticised and being tough."
Chelsea are 10th in the table, but head into the Fulham match having won back-to-back league games for just the second time this season.
Victory could catapult Chelsea above eighth-placed Manchester United but Pochettino said he was not thinking about the table too much.
"For us, it's about to perform and to win. I think at the moment it's not important to be in one position," he said.
"Every single game should be a priority for us. We need to play every single game like a final.
"The most difficult thing is to be consistent, because we're a young team. But we need to try."
