Former deputy defense secretary Paul Thayer yesterday agreed to pay $555,000 to settle civil charges by the Securities and Exchange Commission that he provided confidential information to associates in an insider stock-trading scheme.

Thayer, 65, still is to be sentenced today in U.S. District Court here on criminal charges involving his obstruction of justice by giving false testimony to SEC investigators. He faces a maximum five-year prison term and $5,000 fine.

Dallas stockbroker Billy Bob Harris, who faces sentencing here today on identical criminal charges, agreed to pay $275,000 in the SEC settlement. Another Thayer associate, Texas banker Gayle L. Schroeder, agreed to pay $176,383.

The agreement to repay more than $1 million comes 16 months after the SEC charged the three men and six associates with participating in an insider-trading scheme that netted them about $2 million in illegal profits. Thayer and Harris pleaded guilty to the criminal charges in March in an agreement with federal prosecutors.

Thayer's penalty is unusual because he did no trading in his own name but provided confidential information about companies of which he was a director. Prosecutors have contended that Thayer benefited indirectly by securing profits for his girlfriend, Sandra K. Ryno, 39, whom he was supporting financially.

Harris and Thayer, a former chairman of LTV Corp., had sought to reach a final agreement with the SEC before appearing in front of U.S. District Court Judge Charles R. Richey today. Prosecutors have urged Richey to send both men to prison, but their attorneys have asked that they be sentenced to community service.

Some court observers say Richey generally was considered lenient until June 1982, when he provoked unusual public criticism from prosecutors about what they contended were excessively light sentences for two D.C. liquor board officials convicted of bribery and conspiracy.

Since then, Richey and other judges on the court have given many stiffer sentences to persons convicted of white-collar crimes.

Thayer resigned the Pentagon's No. 2 job days before the SEC lawsuit, saying that the charges were "entirely without merit" and that he would "ultimately be exonerated."

In the consent decree filed in federal court in Dallas, Thayer, Harris and Schroeder neither admitted nor denied the SEC's allegations but promised not to violate securities laws in the future. Thayer and Harris have admitted the insider trading in the criminal case.

Harris, who once touted stocks on a Dallas television show, also was barred permanently from working as a stockbroker or investment adviser.

The commission said it would drop charges against several other defendants, including Ryno, a former LTV receptionist; Juli Williams, a friend of Harris; Thayer's doctor, Doyle L. Sharp, and Sharp's friend, Julia D. Rooker.

The commission said it will continue its case against two other Harris associates. They are Atlanta stockbroker William H. Mathis, a former New York Jets football player, and Malcolm B. Davis, a convicted bookmaker and prominent backgammon player.

The SEC generally places payments such as those to be made by Thayer and his associates into an escrow account to be distributed to those injured by the illegal trading.

Prosecutors say Thayer's associates bought hundreds of thousands of shares in companies that were takeover targets of LTV, Anheuser-Busch Cos. and Allied Corp. They said Thayer, then an official at each of the companies, tried to conceal his involvement by using an assistant's telephone credit card on one occasion and a front man to buy 10,000 shares of stock on another.

Thayer's attorneys said last week that his client did not act out of personal greed but "to provide a small nest egg" for Ryno and her teen-age daughter.

The attorneys produced 68 letters urging leniency for Thayer, including pleas by former president Gerald R. Ford, Senate Armed Services Committee Chairman Barry Goldwater (R-Ariz.) and Gen. John W. Vessey Jr., chairman of the Joint Chiefs of Staff.

Letters urging leniency for Harris included one from James A. Rolfe, the U.S. attorney in Dallas, who said that "Billy Bob has lost everything but his friends." The Justice Department this week repudiated Rolfe's letter, saying he does not speak for the government.

Deputy Attorney General D. Lowell Jensen told Richey that Rolfe had withdrawn from prosecuting the case because of his friendship with Harris.

Jensen said Rolfe's use "of his title, his official stationery and the seal of the Department of Justice was unauthorized and wholly improper."