Senate investigators and auditors from the General Accounting Office have uncovered extensive evidence that federal regulators are failing to protect investors from conflicts of interest, deceptive sales practices and outright fraud in commodity sales.

Two soon-to-be-released government studies raise major doubts about the ability of the Commodity Futures Trading Commission to insure the integrity of the rapidly expanding, multibillion-dollar-a-year commodity business.

The skeptical evaluations of the effectiveness of federal commodity regulation come as Congress today begins deciding whether to shut down the seven-year-old CFTC. Under federal "sunset" legislation, the agency will go out of business later this year unless Congress renews its legislative authority.

The CFTC already is under intense criticism in Congress for its decision to permit the sale of controversial new stock index futures which will allow investors to bet on the rise and fall of the stock market. Stock future sales are scheduled to begin tomorrow.

A draft of the GAO audit obtained by The Washington Post along with testimony prepared for a Senate hearing today show:

* Federal laws that are supposed to protect commodity investors are instead being used to shield swin-dlers from state authorities.

* Commodity markets that are supposed to be "self-regulating" aren't enforcing their own rules, because the federal regulators who should be watching over their shoulder aren't paying attention.

* Privacy regulations meant to prevent disclosure of trade secrets are instead blocking exposure of misdeeds by commodity brokers.

* Routine FBI fingerprint checks that might spot con artists are not being made, permitting persons with previous criminal convictions to register as federally certified commodity merchants.

* A program that is supposed to provide quick, cheap settlement of commodity customer complaints can cost $10,000 and take three years.

The House Agriculture Committee begins three days of hearings today on CFTC reauthorization, while the Senate permanent subcommittee on investigations, chaired by William V. Roth Jr. (R-Del.), starts a series of hearings on commodity fraud.

The commodity commission regulates trading of contracts for future delivery of commodities ranging from corn and soybeans to precious metals, government bonds and now stock portfolios. By buying and selling futures contracts, commodity users try to protect themselves against changes in prices. The market is also widely used by speculators trying to make money by guessing which way prices will move.

Roth said yesterday he fears commodity con men will switch from peddling phony oil and gold investments to the new stock index futures authorized last week by the CFTC.

When Congress set up the CFTC in 1975, it took away all state jurisdiction over any commodity firm or individual regulated by the CFTC. State officials now complain that federal regulation is so weak that swindlers deliberately sign up with the CFTC so local law enforcement authorities can't go after them.

The GAO found that the CFTC does not check the fingerprints of people who apply to be commodity brokers and has no computer system for tracking previous violators. "Since 1978," the GAO report notes, "CFTC has had clear legal authority to require the fingerprinting of applicants for registration, but as a result of the unavailability of essential ADP automatic data processing support has been unable to make use of this mechanism for improving registration safeguards."

The GAO audit is meant to help Congress decide whether the CFTC is worth keeping. The auditor's answer is yes, but. The agency "has achieved notable progress," GAO concluded, but "many of the weaknesses in the program which were described in our 1978 report still exist."

At a hearing last week, Rep. Benjamin S. Rosenthal (D-N.Y.) complained that the GAO had "toned down" its criticism and buried details of CFTC shortcomings in a 200-page report. Because the GAO audit has not yet been made public, CFTC officials decline to comment on it.

The government auditors noted that the last time they looked at the commodity agency they suggested a series of steps to "provide better protection to the trading public from unfit and unqualified individuals and firms. However, nearly four years later, only one of our recommendations concerning registration fitness and qualifications has been implemented."

The GAO auditors criticized two key programs on which the commodity agency depends to protect the public--self-regulation by commodity exchanges and the customer reparations system that is supposed to work like small claims court in settling disputes.

"The reparations program is not meeting its objectives," the GAO said, because "a complaint takes an average of three years to resolve." Reparations cases were supposed to be so simple that lawyers wouldn't be needed, but GAO found "complainants have difficulty understanding the program" and are forced to spend as much as $10,000 on attorney fees.

The GAO reported "weaknesses of a fundamental and serious nature" in the self-regulation of commodity trading by the nation's commodity exchanges. The exchanges are supposed to police their own business while the CFTC conducts periodic "rule reviews" to see the job is done right.

It has been four years since the last CFTC "rule review" of the Chicago Board of Trade and the Chicago Mercantile Exchange, which together handle 75 percent of the nation's commodity business, GAO said. When the CFTC looked at the Chicago Board of Trade's self-regulation efforts in 1978 it found five out of seven programs were "seriously defficient" and said the board showed "contemptuous disregard" for enforcing its own rules.