Book and magazine publishers are trying to protect their publications by suing pharmaceutical and chemical companies that allegedly reproduce and distribute technical material without paying for it.

At issue is payment to the publishers for articles in such journals as "Annals of Surgery" and "Current Microbiology" that are reproduced routinely on office copiers and used in conferences and research projects.

In the first of a planned series of lawsuits, the publishers accepted a settlement with American Cyanamid Co., which agreed to become a subscriber to the publishers' Copyright Clearance Center and "pay copying fees on all copies" of technical material filed there.

The publishers then sued Squibb Co., in a complaint nearly identical to the American Cyanamid case, asking the U.S. District Court in New York to block Squibb from copying protected material unless it, too, agrees to pay for it through the Copyright Clearance Center. Other lawsuits will follow, according to attorneys for the Association of American Publishers.

The publishers are not opposing reproduction of the articles, only the alleged reproduction without payment. Under a system set up by the 1976 revision of the copyright act, the publishers authorize reproduction, without the need for obtaining specific permission, by registering their articles with the Copyright Clearance Center, in Salem, Mass., on the understanding that users of the material will make payments when billed. In exchange for the unrestricted right to reproduce the material, the users are supposed to remit payments to the Clearance Center, which keeps 25 cents of the $1.60 fee for each copy made and remits the rest to the publisher.

"We have been on the missionary trail for 3 1/2 years," said Charles H. Lieb, the New York attorney retained by the Association of American Publishers to represent such plaintiffs as Harper & Row Inc., J.B. Lippincott Co., and John Wiley and Sons Inc. "Last May we were authorized by the publishers to commence suits to test the law. We chose companies which we have every reason to believe are engaged in substantial copying of journal material copyright by our clients."

American Cyanamid, while admitting no copyright infringement, agreed to register with the Clearance Center, pay fees for all material reproduced, and restrict the reproduction of copyright material to "central copying facilities and other attended copying equipment located on Cyanamid premises."