McLachlan said the doctor had been wounded personally by the fallout and conceded the AFL would have preferred his comments had not entered the public arena.
Essendon and the AFL Players' Association criticised Harcourt last Thursday for some of his comments he made, but both the AFLPA and the AFL accepted his explanation that he did not know he was being filmed.
McLachlan said the AFL did sign off on Harcourt's conference presentation, which detailed the lessons learned from the Essendon supplements scandal, but acknowledged the doctor added some flourishes when delivering the content.
McLachlan also said Harcourt's comments did not breach a non-disparagement clause between Essendon and the AFL, agreed to last year as part of penalties levied against the Bombers because of poor governance of its 2012 supplements program.
"My personal view is no. My legal advice is absolutely definitively no and I don't know if I can be any other clearer than that," McLachlan said.
McLachlan said he was not going to provide a running commentary on the ongoing Essendon saga with the issue before the Federal Court.
Both Essendon and James Hird are challenging whether ASADA had the power to conduct a joint investigation with the AFL into the 2012 supplements program.
"One day I will have my say," McLachlan said. "Until then, let's concentrate on running a football competition, let the legal process play out."
Meanwhile, the AFL chief said the Tribunal was the "right place" to adjudicate the clash between Hawthorn's Brian Lake and North Melbourne's Drew Petrie.
The match review panel referred Lake directly to the Tribunal for the incident during last Friday night's game, where he threw Petrie to the ground and grabbed the North Melbourne forward by the throat.
Petrie is also appearing at Tuesday night's tribunal hearing to challenge his own misconduct charge.
The review panel booked Petrie for making unreasonable and unnecessary contact with Lake's face in the same incident.
"I have to be careful - it's going to the tribunal tonight and I'm pleased it's going to the tribunal," McLachlan said of Lake's case.
"That's the right place to hear this.
"I agree - I don't think this is a good look for the game.
"As to whether Brian has done something wrong or is guilty or what his punishment should be, that's a decision for the Tribunal."
- with AAP
