SAN FRANCISCO — Hewlett Packard Co. and CEO Meg Whitman won’t easily knock out an investor class action over the company’s botched 2011 acquisition of British software firm Autonomy Inc.

Mulling aloud motions to dismiss the case, U.S. District Judge Charles Breyer of the Northern District of California said at a hearing Thursday he was inclined to dismiss allegations against some defendants including former HP CEO Leo Apotheker and Autonomy founder Michael Lynch, who briefly served as an HP vice president.

But Breyer showed more reluctance to throw out the case against Whitman, Chief Financial Officer Catherine Lesjak and the Palo Alto–based corporation. “I don’t know what I’m going to do,” he said.

During the two-hour hearing, lawyers for HP shareholders sparred with defense attorneys over allegations that HP insiders hid accounting irregularities at Autonomy from investors. In November 2012, HP wrote down more than $8 billion of the $11 billion acquisition price of Autonomy, citing accounting fraud by its prior management. The day HP announced the write-down, the company’s stock dropped 12 percent, reducing the company’s total value by more than $3 billion, according to plaintiffs.

Breyer’s questioning centered on events after an Autonomy insider allegedly alerted HP General Counsel John Schultz to fraudulent accounting practices. Schultz conveyed the report to Whitman who hired accounting firm Pricewaterhouse Coopers to investigate, according to lead plaintiffs attorney Ramzi Abadou of Kessler Topaz Meltzer & Check. “The question is—and I’ll take Ms Whitman as an example—what did she know and when did she know it?” Breyer pressed Abadou, who had an answer ready.

Whitman was informed of the whistleblower by May 2012 but continued making incomplete, even reckless, public statements about Autonomy, Abadou argued. He pointed to a June 5 media interview with Whitman. Asked to explain Autonomy’s “disappointing results,” the HP CEO referred obliquely to the company’s problems integrating with HP. But in the same interview, she also said, “I have every confidence that Autonomy will be a very big and profitable business.”

That statement was “actionable,” Abadou told Breyer.

But the judge took another view. “She’s looking forward,” he responded. “That’s a forward-looking statement … She could believe it will be profitable.” The bigger issue, Breyer suggested, could be what Whitman didn’t say. “My problem is omission,” he said.

Whitman’s attorney, John Dwyer of Cooley, who appeared by phone, tried to cast blame on Apotheker, HP’s previous CEO. “This was Mr. Apotheker’s deal, not Ms. Whitman’s,” he said.

Companies like HP are approached by whistleblowers “all the time,” he added, and the company shouldn’t publicly respond to every alarm without first investigating.

HP attorney Marc Wolinsky of Wachtell, Lipton, Rosen & Katz pointed to the company’s hiring of PricewaterhouseCoopers to audit Autonomy’s books as a sign the company was trying to understand the problem, not hide it. Wolinsky noted that HP’s management had not concealed disappointment with Autonomy’s performance. “They were not holding back that news,” he said. “It was well known that the company was doing badly.”

“And they turned to HP for an explanation,” Breyer shot back, “and HP gives them an incomplete one. “Breyer also seemed hesitant to dismiss allegations against Lesjak, who as chief financial officer signed off on HP’s filings with the U.S. Securities and Exchange Commission between 2011 and the end of 2012—the period covered by the suit.

The judge compared the company’s statements to a doctor’s diagnosis. “The doctor reports the symptoms. Ms. Whitman gives a diagnosis,” Breyer said turning to Lesjak’s attorney, Wilson Sonsini Goodrich & Rosati partner Steven Schatz. “My question for you is, does your client have any responsibility for the diagnosis?”

“She has responsibility for her statements,” Schatz answered. “Her statements were accurate.”

Contact the reporter at mtaves@alm.com.