Newcastle have announced that Willie Donachie has resigned from his position as reserve team manager.
Donachie had earlier been suspended by the club over an allegation that he hit one of his players.
The Magpies have launched an investigation into an incident after the Under-21 team's 2-0 defeat at Sunderland on Monday evening.
It is understood the 62-year-old former Scotland international's conduct is being probed after it was claimed he was involved in an altercation with 19-year-old defender Remie Streete.
Newcastle's loss in the second-string derby came two days after the senior team were beaten 3-0 at home in the Barclays Premier League by the Black Cats.
The news of Donachie's suspension came as manager Alan Pardew prepared to sit down with owner Mike Ashley to plot a way forward for the club.
The 52-year-old will send his depleted team into Barclays Premier League battle at Chelsea on Saturday after more tumult on Tyneside.
The Magpies sold their best player, Yohan Cabaye, without replacing him, before losing to neighbours Sunderland and then witnessing the departure of controversial director of football Joe Kinnear inside six turbulent days.
The transfer window debacle and the derby defeat proved simply too much to take for some fans, one of whom ran on to the pitch to confront Pardew during the Sunderland game, while others have signalled their intention not to renew season tickets.
However, asked what his message will be when he meets Ashley to discuss life after Kinnear, the manager said: "My message is always the same, it's about taking the club forward.
"We can't stand still, we have to go forward, so it gives us an opportunity to do that.
"Let's be honest, it was an emotional game and the fan running on the pitch with a season ticket and all that, that's what our fans are and they will never take that away from them.
"They are passionate, they love the club and the best thing I can try to do is get the best team I can out there to get results for them.
"I have no problem with that passion. It comes to the surface. There was a bit of frustration this week with season tickets going forward.
"But two years ago, we finished fifth; this year, we are eighth and we have done a brilliant job.
"We have lost a great player, we know that, and in the summer hopefully we can bring three or four great players in. Let's hope so because this club deserves it."