PALO ALTO, Calif. — President Obama will meet here on Friday with the nation’s top technologists on a host of cybersecurity issues and the threats posed by increasingly sophisticated hackers. But nowhere on the agenda is the real issue for the chief executives and tech company officials who will gather on the Stanford campus: the deepening estrangement between Silicon Valley and the government.

The long history of quiet cooperation between Washington and America’s top technology companies — first to win the Cold War, then to combat terrorism — was founded on the assumption of mutual interest. Edward J. Snowden’s revelations shattered that. Now, the Obama administration’s efforts to prevent companies from greatly strengthening encryption in commercial products like Apple’s iPhone and Google’s Android phones has set off a new battle, as the companies resist government efforts to make sure police and intelligence agencies can crack the systems.

And there is continuing tension over the government’s desire to stockpile flaws in software — known as zero days — to develop weapons that the United States can reserve for future use against adversaries.

“What has struck me is the enormous degree of hostility between Silicon Valley and the government,” said Herb Lin, who spent 20 years working on cyberissues at the National Academy of Sciences before moving to Stanford several months ago. “The relationship has been poisoned, and it’s not going to recover anytime soon.”