E. F. Hutton & Co. Chairman Robert M. Fomon testified today that the firm's multibillion-dollar check-kiting scheme resulted from a lack of controls over a number of its branches, not from conscious corporate policies.

Fomon said that in the wake of its pleas of guilty to defrauding banks out of millions of dollars of interest, the nation's fifth-biggest brokerage firm has taken every security precaution "anyone can think of" to make sure it doesn't happen again.

The Hutton chairman was testifying before the Connecticut Banking Department, which must determine whether to impose sanctions on Hutton. Under Connecticut law, convicted felons can have their brokerage and investment-adviser registrations suspended or revoked.

The 2,000 felony mail and wire-fraud counts to which Hutton pleaded guilty in federal court last year involved a Hutton cash-management scheme in which at least 20 of the firm's 400 branches regularly withdrew more money than they had on deposit from their bank accounts. In effect, the banks were tricked into making interest-free loans to Hutton.

Hutton paid $2 million in federal fines, $750,000 in court costs and agreed to make restitution to any bank that lost money from 1980 until 1982, when prosecutors said the scheme was under way.

Fomon said today that he was unaware that the firm was going to be indicted until just days before Hutton decided to plead guilty, precluding a trial.

Although the federal investigation took about three years, Foman said that until the last he thought the most that would happen would be that "they would enjoin us."

In earlier testimony today, the former manager of Hutton's Hartford office said that his branch regularly withdrew more funds than it had on deposit in local banks to "recapture" interest income from those banks. The Hutton deposits were in noninterest-bearing accounts, mainly checking accounts.

But Robert Clark said that he always made sure the banks had sufficient "collected" funds -- cash and checks that had cleared -- that they could lend or invest so that the Hutton business was always profitable for the banks.

Clark is one of several Hutton branch managers who have resigned in the aftermath of the check scheme. He was also ordered by Hutton to pay a $25,000 "fine" to local charities. He remains a broker in Hutton's Hartford office.

Connecticut Attorney General Joseph I. Lieberman, who is pressing the case against Hutton before the banking department, said he believed that testimony from former Hutton employes and current executives, as well as documents he has introduced, demonstrate that it was Hutton pressure on its branch managers that caused some of them to participate in the check scheme.

Clark said yesterday that as much as 75 percent of the $200,000 to $225,000 he earned in 1980, 1981 and 1982 came from his share of the branch's profits. Part of those profits came from the interest derived from the scheme.

But Clark said auditors never looked at his cash-management practices and said top Hutton officials never told him to follow practices that went beyond the guidelines in Hutton's cash-management plan.

Thomas F. Curnin, representing Hutton, said neither federal prosecutors nor former U.S. attorney general Griffin Bell found fault with Hutton's cash-management program -- only with the abuses in the score or so offices. Bell was commissioned by Hutton to investigate the scheme and to make recommendations both for changes in its management practices and for discipline against those responsible.

A number of Hutton officials have resigned, taken early retirement or, like Clark, been demoted. Every disciplined official was told to pay a $25,000 fine to charities, Fomon said, although he said he did not know if all had done so.

Foman said he substantially agreed with the Bell report, which Foman commissioned last spring. The report, issued in early September, described a lack of controls over cash-management practices at Hutton. But the Bell report said that top Hutton executives, like Fomon, did not know of the illegal practices.