The club failed to file its entry and realised its mistake when Football New Zealand released the draw for the preliminary round about a month ago.
The club contacted New Zealand Football in the hope of securing late entry but was declined a place in the centrepiece of domestic football.
"It’s just human error and we can’t do anything about it," Mosgiel coach Craig Whitson said.
"It is not worth blaming the person. They made a mistake and we just have to move on."
Whitson said the team was disappointed it would not feature in the 94-year-old knockout tournament but no-one had "really said too much".
"Everyone has moved on. We will make sure that we are in next year."
Mosgiel is in fifth place in the Southern Premier League with two wins and two losses from four games.
