The Commerce Department has tentatively agreed to provide a $3 million federal loan guarantee to aid financially troubled Auto-Train Corp.

The government-guaranteed loan has been okayed by the department's Economic Development Administrations, while another federal agency, the Securities and Exchange Commission is pressing to complete a broad, year-old investigation of the company's operations.

"We gave them a draft loan guarantee agreement," said Glenn Waldron, the EDA official handling the Auto-Train loan request. "Our intent - if they can do this according to the conditions we set - is to go ahead with the deal."

The loan guarantee will allow Auto-Train to borrow the $3 million from a private lender, with the promise that if Auto-Train is unable to repay the debt, the federal government will make good on the loan.

Auto-Train has been unable to pay debts to several major creditors recently, and the creditors have given the railroad more time to pay in order to keep Auto-Train in business.

Auto-Train has lost money for three years in a row and applied for the EDA-backed loan this spring after private efforts to raise funds were unsuccessful.

The Washington-based railroad sought the federal aid under an EDA program designed to help preserve and create jobs.

At least $1.33 million of the $3 million Auto-Train hopes to borrow will go directly to the Seaboard Coast Line Railroad, Auto-Train's biggest trade creditor, financial reports filed by the company disclose.

Auto-Train officials have said they hope to use part of the federally guaranteed funds to pay for extending the northern end of their route from the Virginia suburbs to Newark, N.J., and to expand the company's rail-car repair business.

FDA officials insisted yesterday it is not unusual for the government agency to guarantee loans to financially troubled companies or for much of those loans to be used to pay off old debts.

"We don't consider this a bail-out," said Waldron. "What we're doing is trying to give them capital to keep the wolf away from the door. If they're not an ongoing concern, they can't create any jobs."

Auto-Train Exeecutive Vice President Richard Goldstein said yesterday two company officials are negotiating with a private lender to make the government-guaranteed loan.

Waldron said the terms EDA has imposed on the Auto-Train loan are not a matter of public record.

In an amended financial report filed recently with the SEC, Auto-Train disclosed that $333,00 from the loan will be used to pay a Seaboard Coast Line bill that was due May 15. The SCL provides the tracks and train crews for most of the Auto-Train route from Lorton, Va., to Sanford, Fla. SCL agreed to give Auto-Train more time to pay its bill on the condition it be paid out of the government-guaranteed loan, the SEC report discloses.

Another $1 million from the EDA loan will be put into an escrow account under control of the Seaboard to pay other claims against Auto-Train, the SEC filings show. Auto-Train will also have to pay 2 percent of its gross revenues directly into the Seaboard escrow account.

The railroad also is negotiating with an insurance company for another $3 million loan that would be use to pay off an earlier $3 million loan from American Security Bank. Because of Auto-Train's financial condition, that loan has been guaranteed by some of the company's major suppliers, including Marriott Corp. and the Seaboard.

Auto-Train lost $4.42 million ($2.69 per share) in 1978 and recorded another deficit of $663,000 (40 cents) in the first quarter of 1979. It lost $520,000 in the fiscal year ended April 30, 1977, and another $2.54 million in an abreviated fiscal year ended Dec. 31, 1977.

Since December 1977, the company has been the target of a private SEC investigation. Sources close to the investigation say the SEC has probed alleged illegal political payments by the company, possible illegal use of company funds and alleged insider dealings in Auto-Train stock.

Although Auto-Train has announced publicly that it believes the investigation is being concluded, SEC attorneys recently obtained subpoeanas for records of at least one former Auto-Train baord member and have questioned several former employes of the company.

Auto-Train's stock, which had been severely depressed because of the company's poor fiscal performance, took off a few weeks ago on the basis of reports that gasoline shortages would bring the company business.

The stock jumped from 1 7/8 to more than $7 a share in trading on the American Stock Exchange, then cooled off and drifted down to the $4 to $5 range this week.

Goldstein said yesterday the company's reservations are running substantially ahead of last year and "business is great." He said Auto-Train booked 920 reservations on Monday, compared with only 199 on the same date a year ago. Goldstein projected the train will carry about 1,200 more automobiles this month than it did last June, one of its worst months ever.