The Securities and Exchange Commission slapped E. F. Hutton yesterday with a series of civil penalties for the same check-kiting scheme that resulted earlier this year in the giant brokerage firm pleading guilty to 2,000 criminal fraud charges.

The agency prohibited Hutton from opening any new retail brokerage offices for 120 days, ordered a series of new internal controls to prevent future cash management abuses and said it will hold hearings on whether Hutton should be disqualified from serving as an investment advisor."

And in another unusual step, the SEC said it will not end its involvement in the case. Instead, it severely criticized laxity in senior managers and said it will continue to investigate "in order to determine whether enforcement actions against individuals or other entities are appropriate."

Hutton consented to a court order enforcing the SEC penalties, but neither admitted nor denied it had violated federal securities laws.

Hutton is Wall Street's fifth-largest brokerage house and has about 400 offices across the country. The ban on opening additional branches will remain in effect while an independent consultant examines Hutton's practices and policies. Hutton agreed in advance to accept any of the recommendations that the agency wants implemented.

The SEC's decision to keep the case open and possibly take action against individuals was termed "significant" by Rep. William J. Hughes (D-N.J.), chairman of the House Judiciary subcommittee on crime.

Hughes' panel will resume its continuing inquiry tomorrow into the Justice Department's decision not to prosecute individuals in the Hutton case. While the Justice Department's decision prevents the SEC from pursuing criminal prosecutions, the agency has kept open such options as taking away individuals' brokerage or investment-adviser licenses, Hughes said.

Similarly, Irwin Borowski, a former associate director of the SEC's division of enforcement who is now in private practice, called the decision to continue the Hutton case "possibly the most important aspect of what the commmission did."

The Justice Department has said it decided to prosecute the company rather than individuals primarily to win its consent to the guilty plea, to a permanent injunction barring a broad range of cash-management practices and to obtain a restitution plan for victimized banks. The department said the outcome better served the public than would have the perhaps-unsuccessful prosecution of middle-level officials.

The SEC's action yesterday included a temporary extension of Hutton's authority to act as an investment adviser. Under the Investment Company Act of 1940, the agency could have disqualified the firm because of the felony convictions. A 180-day temporary exemption granted May 2 -- the day of the guilty plea -- would have expired yesterday. The SEC said it will hold hearings on Hutton's request for a permanent exemption from disqualification.

The SEC action requires Hutton to pay more than $1 million to shareholders of Hutton-managed investment companies who earned less interest than they should have because investments in their accounts weren't credited promptly. The company said it has already paid out the money.

The SEC said it based the enforcement actions on Hutton's "failing to disclose the financial effects of cash-concentration practices and failing properly to administer investment company operations."

A Hutton statement described what it called "an all-inclusive settlement" stemming from a six-month SEC investigation.

As part of the settlement, Hutton's agreed to abide by a permanent civil injunction designed to assure that it will maintain adequate internal controls and make all financial disclosures required by the SEC in its quarterly and annual reports to the agency. Failure to comply with the injunction could subject Hutton to future penalties.

Hutton's annual reports for 1981 and 1982, the SEC alleged, failed to reveal over-drafting abuses that materially affected its profits. The practices inflated by $3.5 million the increase in the company's profits from 1980 to 1981.

Hutton Chairman Robert M. Fomon issued a statement saying, "We are gratified to have resolved the cash-concentration issue with our principal regulator" and "encouraged that the SEC's characterization of the financial impact of the improper practices and the manner in which those practices developed is consistent both with Judge Griffin B. Bell's findings and the company's own findings."

Fomon commissioned Bell, a former U.S. attorney general, to investigate the practices that led to the guilty pleas. Among other things, Bell's report criticized former chief financial officer Thomas P. Lynch for having "failed in his responsibility to ensure that adequate controls were established . . . . "

Yesterday, however, the company said that the SEC-approved consultant will evaluate its policies and practices and, "in the context of prevailing industry practices, Hutton obligations to its customers, and existing law and regulations."

"Our most fundamental obligation as a firm is our duty to our customers and clients," Fomon said. "We also have obligations to our shareholders, and we must balance those loyalties on a daily basis. Our view is that an inquiry into the practices of Hutton and its peers can only be constructive."

SEC Chairman John S. R. Shad, a former Hutton vice chairman, did not participate in the actions.

Meanwhile, Massachusetts barred Hutton yesterday from selling limited partnerships and tax shelters there until Jan. 1 as punishment for selling unregistered movie industry securities.