The confidential memorandums, which were sent by computer from Waldenbooks' corporate headquaters in Stamford, Conn., to all of its stores, did not refer directly to the Ayatollah or his threats, but said, ''We feel this measure is necessary due to extensive negative press.'' Employee Safety Stressed

The follow-up memo made it clear that employee safety was the sole consideration, and left up to managers the decision whether the book should be sold under the counter. The memorandum also instructed managers not to return copies of the book to distribution centers of the American publisher, Viking Penguin.

The first message from Waldenbooks was unsigned and described as ''urgent.''

''Until further notice,'' it said, ''remove all copies of 'Satanic Verses' (Viking) from your shelf and hold in your back room.'' It also said: ''If anyone asks about the book, ask them if they're with the media. Do not answer any media enquiries and do not give your name. Just say no comment. This is our corporate statement.''

The manager of a company store in Connecticut said the book could not be ordered through the Walden chain. A Waldenbooks employee in Los Angeles said, ''They were called back throughout all the stores.'' A Day Off at Viking Penguin

Also yesterday, the second anonymous bomb threat in two days disrupted the Manhattan headquarters of Viking Penguin, the publisher of ''The Satanic Verses.''

After the bomb scare, the company gave its employees Friday off. In a memorandum, Viking Penguin officials praised them for their efforts ''under trying conditions,'' and attributed the extra day off to the feeling that ''we all could use a little bit of additional time for some rest and relaxation.'' But people in the company said the publisher will also use today and tomorrow to install a security system.

Despite the Waldenbooks decision, Mr. Rushdie's novel is selling fast at many other American bookstores.