Metro's newly appointed auditor-general said yesterday that he is alarmed by what appear to be lax practices employed by the multibillion-dollar transit system in handling money and costly equipment.

In his first public statement since taking over as chief watchdog, John D. Heller warned that the transit authority may lack safeguards to prevent theft and other abuses. "That's something that alarms me," said Heller, a former assistant comptroller general of the General Accounting Office, who was hired by Metro two months ago.

Heller cited several possible shortcomings. He said it is unclear whether employes who have access to cash or sensitive computer operations are adequately screened to avoid security risks. He said that bus and rail equipment appears to be removed from the authority's inventories when it is being repaired, raising prospects that an item might disappear without any record.

Heller recalled having seen valuable Metro equipment that appeared to lack any property control sticker. "Is that under proper control?" he asked."If you don't have an accounting control, it might walk out the door."

Metro has sought to clamp down on fiscal practices, partly as a result of a 1982 report by the U.S. Transportation Department's inspector general, which described the agency as vulnerable to fraud and other abuses because of lax management controls.

Heller's comments, at a Metro committee meeting and in a later interview, came amid two other developments yesterday dealing with security and management issues at Metro:

* Officials outlined a series of measures now under way to reduce fare evasion and thefts from fare collection machines on buses and in subway stations. According to recent estimates, the Metro system loses $7 million a year or more from thefts and underpayment of fares. The new crackdown, officials indicated, has already cut losses by thousands of dollars.

* Officials also disclosed two key findings in a report now being prepared by GAO, Congress' auditing arm. The study, which has not yet been made public, centers on Metro's purchase of 294 Italian-made rail cars for about $275 million.

Officials from both agencies confirmed that GAO had criticized Metro for failing to establish a plan for testing the new cars to ensure that they operated satisfactorily. GAO also objected to Metro's decision to exercise an option to buy the final 200 cars before the transit agency received and examined any of the first 94 cars from the Italian company.

Metro officials reportedly disputed these contentions, arguing that a testing program has now been established and that the transit authority had little choice but to exercise its option to buy the additional cars because of an impending deadline. Failure to exercise the option, these officials reportedly argued, might have led to higher costs for rail car purchases.

In the interview, Heller said he had uncovered no evidence of criminal wrongdoing during his preliminary examination of the transit authority.

He also noted that his information in many areas is not yet complete. "If I do an audit of them, they may not turn out to be as bad as they seem," he said.

To reduce theft and fare evasion, Metro officials said they are relying on improved surveillance techniques, more stringent record keeping and new security devices.

On buses, Metro plans to test 10 new fareboxes outfitted with noisy alarms and flashing lights that would be triggered by any breakin attempt. In Montgomery County, Metro is trying out 23 electronic fareboxes that alert drivers if passengers fail to deposit correct fares. Automated transfer dispensers are being tested on five D.C. buses, partly in an attempt to deter transfer thefts.

In rail stations, Metro is readying new electronic devices designed to detect fare card fraud and use of obsolete flash passes. Protective handles are scheduled to be installed on fare card vending machines to prevent burglaries. An alarm-triggering apparatus is also being tested for possible use on vending machines.

Burglaries from rail stations climbed from $124,324 in 1981 to $143,794 last year, but dropped to $21,553 so far this year, with none reported since mid-February, according to Metro officials. Theft from vending machines by Metro's own employes declined from $58,336 in May 1982 to $37,399 last month, Metro officials said.