"We've been pretty ambushed by this today," Lynch said in an interview from London. "I think there's been significant mismanagement of the company."
Lynch's comments came after HP said earlier Tuesday that it was forced to take an $8.8 billion one-time charge because of "serious accounting improprieties" at Autonomy, which HP acquired for $11.5 billion in 2011.
The news surprised investors and sent HP's stock (NYSE: HPQ) plunging.
In a separate interview with CNBC on Tuesday, HP CEO Meg Whitman, who fired Lynch shortly after the Autonomy acquisition, said the company engaged in a "willful effort to mislead" HP shareholders and management.
For his part, Lynch said the mismanagement came after HP took over the company.
The due diligence-or checking the books-on Autonomy "was what Hewlett-Packard described as meticulous," said Lynch. " And then they actually ran the company, including doing all of the books, for the last four quarters."
"We'd be talking about a massive elephant in the room that wasn't spotted," he added. "And the reason it wasn't spotted is very simple - it wasn't there."