Nketiah was set to join Augsburg on deadline day, with a loan deal planned until the remainder of the season.
But Ljungberg says Emery nixed the plans because he sees Nketiah as an important part of his team.
"There's a lot of rumours about what happens," Ljungberg told football.london. "What happens behind the scenes stays behind the scenes. If the club or Eddie wants to make a statement that's a different story.
"The main thing for Eddie is that he stayed because he's so important to Unai that he wants to keep him.
"He should see that as a pat on his own back that he's important to the club even if there were offers for him to go.
"That decision was up to Unai and the big bosses. It's nothing to do with us."