His report to the anti-doping authority will not be made public as it is part of the ongoing ASADA investigation.
Once Downes hands in his report, the anti-doping body will decide whether to proceed with any action.
"My best understanding is that decisions around show-cause letters, or not, will be in the back half of May," McLachlan said on Tuesday.
McLachlan was one of the key figures on the AFL side of the joint investigation with ASADA into Essendon's 2011-12 supplements program.
He would not be drawn into the particulars of the negotiations with Essendon last August but admitted the tumultuous saga had taken its toll.
"I'm sure there was some skin taken off me - there was some skin taken off a lot of people," he said.
"It was an incredibly tough period in the history of our game.
"We ended up in a position that I don't think was edifying for a lot of people and it certainly wasn't great for our game.
"It probably did take some bark off me."
McLachlan added events of the last year had made it clear that the AFL had to be more transparent with how it handled such major issues.
"A key learning out of last year is that process and transparency are going to have to be prioritised ... rather than what we think is the right solution for the game in the short term," he said.
The AFL hit Essendon with unprecedented penalties, kicking them out of the finals and banning coach James Hird for 12 months.
The Hird camp remains extremely bitter over how the AFL treated him.
Hird is scheduled to return as Essendon coach in August and McLachlan acknowledged the need to make peace with him.
"It's incredibly important that we move forward with Essendon and every individual there (at Essendon)," McLachlan said.
"I'm sure at the right time, when James returns, we will take and we will move on, because that's what the industry and Essendon need."
AFL commission chairman Mike Fitzpatrick said the League was conducting an extensive review of how it handled the Essendon investigation.
"I have got a very good sense of the shape of it, but it would be a bit premature to announce it today," Fitzpatrick said.
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