ESSENDON senior assistant Mark Thompson says the Bombers and the AFL are whittling down the charges laid against the club, but the parties are yet to come to a resolution. 

Thompson left AFL House shortly before 7pm after six hours of negotiations between Essendon officials and the League.   

He said he would be returning to AFL headquarters on Tuesday morning to continue discussions. 

"I'm not sure if the Essendon deals will get done tonight," he told Fox Footy's AFL 360

"When I left half an hour ago they were the same distance away that they were two hours ago, three hours ago. 

"We're trying to scrub off as many [charges] as we can to be responsible and to be charged for what we think we are responsible for."

On Monday night, Essendon was facing penalties that Thompson said were "probably more severe than anything ever in history".

He said the club was looking after its interests, and Thompson, coach James Hird, football manager Danny Corcoran and doctor Bruce Reid were defending themselves.  

He said the club and its officials had been reasonable through Monday's negotiations. 

"I would say the fines and the punishment the club is going to receive, based on what I've heard the last couple of days, is quite severe," he said.  

"Then you look at it and you say, 'Well, we actually haven't been charged, we've broken no AFL rules or codes, and no players have used prohibited substances'. 

"For us to accept what we're being offered I think is being very generous and kind."

Thompson said he was prepared to accept a penalty for his role in Essendon's supplements saga, but he would not accept charges that paint him as a drug cheat.   

"I'm fighting for my reputation, my integrity, and I want to clear my name," he said.  

"I think what's on the charge sheet – and I only received my final one on Sunday night around eight o'clock – even from that there's 80 per cent of it I want to fight.  

"Unless it really gets serious and reflective of what I'm responsible for, then we're going.

"At the moment [my penalty] is a fine, but if we don't agree to it, to what the AFL are handing out, then that might be off the table and we go back to a suspension or whatever it is."

Thompson spent Monday at AFL House from 1pm with his lawyers and said he met with the AFL Commission twice, but only to ask for more time. 

He said the AFL lawyers spent more time with the Essendon and Hird camps, but it was unclear when the senior coach's penalties would be confirmed.  

"I know that he's defending his reputation and integrity too and he's being quite stern," Thompson said.  

"I think he's got the support of our Essendon people. If he was to lose 12 months it would be disastrous. 

"He is a young coach who is learning his way, and he didn't deliberately set out to do anything wrong. 

"If the AFL knocked him out for 12 months that he would struggle to want to get back."