Former attorney general Griffin B. Bell yesterday blamed top executives of E. F. Hutton & Co. for allowing an illegal check-overdrafting scheme through "loose management," but cleared them of criminal wrongdoing.

Nonetheless, three top executives, including Hutton's chief financial officer, are leaving the company as a result of Bell's three-month-long investigation, which was ordered by the Wall Street firm after it pleaded guilty to Justice Department charges of 2,000 counts of mail and wire fraud. Two other executives will be reprimanded, and nine regional and branch managers will be punished by suspension or fines as high as $50,000 to be paid to charities.

"We tried to link the high officials at Hutton with the wrongdoing. We were never able to do that from a standpoint of criminality," said Bell, an Atlanta lawyer who served as attorney general in the Carter administration. Bell presented the results of the investigation at a 90-minute press conference here in which his 183-page report and a two-inch thick appendix of documents were released.

He said there was "criminal wrongdoing" on lower and middle levels of the company, where a "greed instinct took over," leading regional and branch managers to boost interest income for Hutton through "abusive" and illegal banking practices that included "excessive" overdrafts. Branch managers received bonus income as a result of increased interest earnings, which the Justice Department estimated amounted to hundreds of millions of dollars.

Hutton's emphasis on promoting interest income, which at times in 1982 amounted to more than stock and bond revenue at Hutton's Alexandria branch office, created "an overdraft culture" at the firm, Bell said.

"Overdrafting became tantamount to a loose cannon, fired at will by a minority of Hutton employes," said Bell.

"It was a management failure, not an ethical failure" on the part of high-level company officials, he said later in the press conference, in which he was challenged repeatedly for not recommending that stronger sanctions be taken against top executives. Bell said Hutton Chairman Robert Fomon acted ethically once he learned of the schemes by pleading guilty to the federal charges, showing "remorse" and taking action to get "the problem behind him."

Rep. William J. Hughes (D-N.J.), chairman of a House Judiciary crime subcommittee investigating Hutton, criticized Bell's report for clearing the company's top executives. He said his subcommittee investigation showed "criminal knowledge" of the illegal check-overdrafting schemes "at top levels of the corporation."

Bell recommended stiff punishment for only one top executive in Hutton headquarters, Thomas Morley, the "money mobilizer" who was in charge of managing company funds to maximize interest income. Although Bell recommended that Morley be retained but barred from any job involving money management or banking, Fomon announced in a terse sentence in the company press release yesterday that the money manager "is leaving the company."

Two other Hutton officials are giving up their executive positions but remaining on the corporation's board of directors. They are Thomas P. Lynch, executive vice president who was de facto chief financial officer in 1981 and 1982, and Thomas W. Rae, who will take early retirement from his post as general counsel to go into private law practice.

Two other top officials will receive reprimands. They are Richard G. Genin, a senior vice president, who Bell said failed to supervise regional officers, and Ernest Dipple, a regional sales manager and now a vice president, who Bell said should have known that branch managers were running excessive overdrafts in their bank accounts.

Among six branch managers singled out for punishment were Perry Bacon, who headed the Alexandria office and now is based in Washington; Anthony Read, who headed Hutton's Baltimore office, and John Pearce, who headed offices in Bethesda and St. Louis. They will be fined between $25,000 and $50,000, to be given to charity. As a charitable contribution, their fines are tax deductible, Bell said.

"We have concluded that the conduct of the managers of these six branches was such that no reasonable person could have believed this conduct was reasonable," Bell said.

He called the punishment "fair" and "more than a slap on the wrist. It's a sizable sum" for the branch managers, who he said earn more than $100,000 a year each.

In what is likely to be the most controversial section of the report, Bell said he found no reason to blame Fomon, the chairman of Hutton, for the illegal activities of his underlings.

"Fomon is not accountable for failing to supervise Morley or any other person with regard to money management. Fomon is not responsible for the failing of Hutton officers and employes to implement the appropriate internal accounting controls to monitor the cash management system," the report said.

As chief financial officer, Lynch, however, "should have been aware of the potential abuses of overdrafting," Bell concluded. Under sharp questioning over his treatment of Hutton's top executives, Bell commented, "See if Lynch thinks he was exonerated."

Rea, the chief counsel, also was criticized for failing to exert proper control over his departments, especially with regard to fully complying with a Justice Department subpoena.

While both of those men are leaving the company, Bell said the stockholders will have to decide whether they keep their seats on the Hutton board. Although he called the investigation "a public inquiry," Bell said it would be "gratuitous" for him to make a recommendation to the stockholders on that question.

Bell declined to say how much his investigation would cost Hutton, although he described his fee as "substantial." He said 14 attorneys and four paralegals from his Atlanta firm, King & Spalding, worked on the investigation.

He insisted that his investigation was not tainted because he was hired by Fomon and is being paid by Hutton. "I don't feel like I was being used," he said.