The AFL fined the Bombers $20,000 for the club's players wearing yellow armbands in support of cancer awareness in Sunday's match against Melbourne at Telstra Dome in defiance of a clear directive from the league.
Essendon had requested permission from the league to wear the armbands - which they hoped would raise awareness of the illness and show support for cancer-stricken teammate Adam Ramanuaskas - but the AFL knocked the Bombers back, citing precedent in that other clubs have been denied similar requests.
Jackson called for AFL CEO Andrew Demetriou to personally step in and take control of a situation.
"The AFL is mean spirited," Jackson said at Windy Hill on Tuesday.
"I think they got it wrong this time. They got caught up in procedures and processes and precedents… and rules," he said.
"Sometimes the AFL has got to show that football is more about just rules and precedents. It's about people and it's about passions and that's where I think they are mean spirited."
Jackson felt the AFL didn't understand or take on board what the Essendon Football Club was trying to achieve, believing they mistook the Bombers' actions as nothing more than a PR exercise.
"We tried to explain from the very beginning since this came up, this wasn't about a promotion about the cancer cause," Jackson said.
"That happened to be a coincidence.
"What was behind this issue was that there were a group of players who feel very passionate about their mate, who they played a premiership with, and they wanted to show him their support.
"At the end of the day the AFL wasn't listening to what we were talking about.
"I personally kept getting confronted by this issue that we were talking about promoting cancer awareness. I tried and I got very frustrated, to be honest to be with you.
We are not talking about that. This is about a group of players eight or ten in particular, who felt passionate about their mate. Will you please forget about it being a promotion of the game," he said.
"It was not a PR exercise. What was put to me was previous clubs were knocked back for promotional reasons and we kept trying to say, this is not about promotions.
"Once a group of players get passionate about something like that, I'm not going to defy them. I'm just not," Jackson said.
Jackson, while angry with the decision, threw his support behind the players and was happy to pay any fines the players or club may receive.
"Essendon Football Club supported the players in this decision; I supported them and told them I would, so the club will pay the fine.
Jackson had all but ruled out appealing, declaring there were no avenues open to the club.
"We don't have an appeal process because the fine is made under the AFL regulations, not under the player rules.
"We've had a look at the rules and certainly, we think at this stage, and we'll be putting a submission in that the authority is only to (fine the club) $5000."
"Whether we win that argument or not remains to be seen," he said.
Asked for his thoughts on how the players and public felt, Jackson said: "I think everyone's bewildered. The level of support we've got is quite extraordinary.
"It's the first time we've ever heard Carlton and Collingwood, let alone St Kilda and Adelaide supporters, actually emailing this club and wanting to get behind us.
"They suggest a show of public support at the next full round of games to make a statement about this. It's quite extraordinary.
"I must admit I didn't anticipate that happening at all," Jackson said.
Jackson called on the league to match the Bombers' $20,000 fine and to donate it to the Anti-Cancer Council.
"Perhaps the AFL can match it and prove they're not mean spirited. Maybe the Cancer Council can get $40,000 and then we can get something useful out of this exercise," Jackson said.
