The Treasury Department makes double payments on more than 100,000 government checks a year and has made no attempt to recover about $73 million in such payments made over the last three years, internal Treasury and Secret Service reports show.

The double payments are made when Treasury is told by intended recipients that their checks never arrived or were lost. If the check has not already been cashed, Treasury issues a replacement check, but does not stop payment on the original check.

The original check is often cashed fradulently, either by the intended recipient or by a forger.The Secret Service report, dated last July, and the Treasury report, prepared in September, show that Treasury has failed to take steps to recover most of the money lost in this way.

The backlog of such cases now stands at $86 million, nearly all of it representing double payments made in the last three years, Treasurey officials acknowledge. About $13 million of this total was wrongly paid out as far back as 1970.

Treasury officials say they do not stop payment on missing checks because they cannot legally do so.

"We are not happy that we built up this backlog, because it increases the chance that we will never recover the money," Dario A. Pagliai, commissioner of Treasury's bureau of government financial operations, which issues government checks, said yesterday.

Pagliai said double payments are made on about a quarter of the reports of lost checks. He estimated that about a third of those double payments occur because of forgeries.

"The reason for the backlog is because of pressure to get replacement checks out promptly," he said, noting that many of the checks go to destitute individuals. Treasury issues checks on behalf of the Social Security Administration to recipients of welfare and old-age benefits. It also issues payroll, Internal Revenue Service refund and contractor payment checks.

"We've added 100 temporary people (to the unit that handles the double payment cases)," Pagliai said.He said this brings the total work force assigned to cleaning up the backlog to 135.

"we have established a target of December 1980 to clean it up," he said.

Treasury now refers 6,800 cases of suspected forgeries to the Secret Service for investigation each month, compared with 2,027 cases last April, he said.

Gerald Murphy, Treasury's deputy fiscal assistant secretary, said Treasury cannot stop payment on checks the way companies or private individuals stop checks by notifying their banks.

He said Treasury checks are like cahshier's checks, meaning the issuer cannot stop payment.

In its report, the Secret Service which is charged with recovering overpayments that occur because of forgeries, attributed the backlog management to focus on the problem, a lack of staff and adequate training, and an absence of "sound" procedures for dealing with double payments.

Treasury issues 600 million of the nearly 700 million government checks written each year. The average check which is paid twice is estimated by the Secret Service to be $200.

However, an internal Treasury report last August referred to a double payment of $200,000 made to a United Nations organization through the U.S. embassy in Rome. In this case, the money was recovered.

When a double payment is made, the Secret Service may collect the funds from the bank that erroneously cashed a check if it was forged or agencies may withhold future payments from intended recipients of the checks.

Even when Treasury refers a double payment case to a government agency, it may not stop future payments, Pagliai said.

When a recipient has been paid twice, "The agency should say, 'you don't get a check until the next month.' The problem is, they're often destitute," Pagliai said.

He said it is Treasury policy to immediately issue a substitute check when the first check is reported missing. On welfare checks, he said, no attempt is made to find out if the first check has already been cashed in order to speed issueance of a new check. "We issue welfare check substitutions in 24 hours," he said.

He estimated a third of the double payments are made because of forgeries, while the rest occur because the intended recipients received a substitute check and cashed the original.

The double payments will be explored at a hearing Thursday by the House Government Operations' Intergovernmental relations subcommittee, headed by Rep. L.H. Fountain (D-N.C.).

The backlog in double payment cases came to light when the Secret Service noticed a dramatic decline in the number of cases referred to it for investigation. The Secret Service assigned a team of agents to investigate last April.According to the Secret Service report, the agents were inundated with complaints from Treasury employes assigned to handle the cases.

The employes alleged that other Treasury officials had deliberately hidden items in the backlog. The agents found a number of cases that should have been disposed of dating back to 1970. They also heard complaints that the Treasury operation was mismananged, did not stand up to banks that refused to cooperate in efforts to track down fraud, and did not have accurate statistics on its operations.