It comes after 34 show-cause notices were reportedly issued to current and former Essendon players.
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Speaking on 3AW, McLachlan said the AFL had not been contacted by ASADA before the notices were made public late Thursday night.
"This process is hugely challenging - it's hugely challenging for the AFL to have no control or visibility over it," McLachlan said.
He did caution that while the notices were only the first stage of a long and arduous process, it had the potential to cause the same disruptions as last year.
"This is nothing more than an allegation to which the players will respond. We will see where it goes. However, I can see it will have an impact on our season."
"It is what it is…and I have great empathy for the players."