The club came under investigation last week when it emerged unlisted players had trained with them before last month's rookie draft.
AFL investigations manager Ken Wood found that Essendon "through a procedural documentation issue, had breached the List lodgement Rules."
Half the fine was suspended through to the end of next year.
The AFL fined Essendon $2 million in late August and kicked them out of the finals over their supplements scandal.
The Bombers have also been in the spotlight this week over media revelations about the backroom negotiations that took place before the AFL announced the penalties.
Essendon are in significant debt for the first time in club history because of their move to a new training and administration centre at Melbourne Airport.