For Leo Apotheker, the former HP chief executive who spearheaded the company’s $11.1 billion acquisition of Autonomy, the news that HP had to write off $8.8 billion over accounting irregularities with the subsidiary must have hit hard.

Apotheker, not surprisingly, is receiving much of the blame for not properly vetting Autonomy. During HP’s earnings call today, current CEO Meg Whitman said “the two people who should have been responsible for the problems are gone” — referring to Apotheker and former chief strategy officer Shane Robinson.

But in a statement to the Wall Street Journal, Apotheker seemed surprised by Autonomy’s financial irregularities, and noted that the “due diligence process was meticulous and thorough” for the deal. While he vows to offer assistance to HP, his statement also cleanly skirts some responsibility on his part:

I’m both stunned and disappointed to learn of Autonomy’s alleged accounting improprieties. The developments are a shock to the many who believed in the company, myself included. But I also share the sentiment of HP’s current leadership and continue to believe in Autonomy’s market potential, as its core software expertise remains sound.

Looking back on the acquisition, which closed in Sept. 2011, the due diligence process was meticulous and thorough, and included two of the world’s largest and most respected auditing firms working on behalf of HP. Since Autonomy was a public company in the UK, much of the process relied on public financial reports — accounting statements approved, filed and backed by Autonomy’s leadership, board and auditors.

According to HP, the accounting issues it discovered pre-date its acquisition of Autonomy. As such, it’s apparent that Autonomy’s alleged accounting misrepresentations misled a number of people over time – not just HP’s leadership team, auditors and directors. In fact, the alleged improprieties apparently came to light only after an internal whistleblower raised the issue in the spring, well after my departure.

I will make myself available, however I can, to assist HP and the appropriate authorities get to the bottom of this.

Apotheker, who also served as SAP’s CEO for two years, was widely criticized during his reign for not understanding HP’s core business. He pushed to kill the company’s WebOS hardware just a year after the company bought Palm for $1.2 billion, and he also brought up the idea of spinning off HP’s PC business. HP ended up open sourcing Web OS, and current CEO Whitman squashed plans for breaking out its PC division.

Photo: HP

HP barely squeaked by analyst expectations in its fourth quarter earnings, but the bigger news today is that the company was forced to take a $8.8 billion charge over accounting irregularities with its enterprise software outfit Autonomy.

Yes, that’s after HP paid $11.1 billion for UK-based Autonomy last year, and it’s on top of the $8 billion goodwill write off the company announced back in August. Altogether, HP announced almost $17 billion worth of charges this year over companies purchased by past CEOs.

The company said the Autonomy charge was over “serious accounting improprieties” — and I’m sure this isn’t the last we’ve heard of this story. It could have been worse, if HP was completely unaware of the accounting issues, or if it tried to bury the story, investors would have even less faith in the software giant.

Update: In a later statement on the Autonomy situation, HP said that it launched an internal investigation after a senior-level member of Autonomy’s management team came forward and noted that there had been “a series of questionable accounting and business practices at Autonomy prior to the acquisition by HP.”

And for the kicker, the accounting issues may have led to HP paying a lot more for Autonomy than it was actually worth. From HP’s statement: “As a result of that investigation, HP now believes that Autonomy was substantially overvalued at the time of its acquisition due to the misstatement of Autonomy’s financial performance, including its revenue, core growth rate and gross margins, and the misrepresentation of its business mix.”

On its earnings call with investors this morning, HP chief executive Meg Whitman said “the two people who should have been responsible for the problems are gone” — referring to former HP CEO Leo Apothekar and chief strategy officer Shane Robinson. She later added that HP’s internal investigation is ongoing, and it has also turned over the case to the SEC in the U.S., and the Serious Fraud Office in the United Kingdom. While a solution will likely take some time, Whitman said the company will figure out a way to make it up to investors.

On the bright side, HP’s earnings per share for Q4 were $1.14, slightly up from analyst estimates of $1.12 per share. Revenues were $30 billion for the quarter, down 7 percent from a year ago, and around $500 million less than what analysts were expecting.

Here’s HP’s official statement on the Autonomy fiasco:

HP is extremely disappointed to find that some former members of Autonomy’s management team used accounting improprieties, misrepresentations and disclosure failures to inflate the underlying financial metrics of the company, prior to Autonomy’s acquisition by HP. These efforts appear to have been a willful effort to mislead investors and potential buyers, and severely impacted HP management’s ability to fairly value Autonomy at the time of the deal. We remain 100 percent committed to Autonomy and its industry-leading technology.

Photo: Devindra Hardawar/VentureBeat