The battle between the Reagan administration and the federally funded program of free legal assistance to the poor has been rekindled by an administration initiative, begun last summer, to send large teams of investigators to individual programs to scrutinize their files and operations.

Opponents of the new audit system have called it a "witch hunt," arguing that the audit teams have disrupted operations in the offices they visit, often demanding to see confidential client files and insisting on being given copies of tens of thousands of documents. In one instance, one of the auditors was a former defendant in a lawsuit brought by the legal-services office he was auditing.

"They're fishing for evidence of some wrongdoing so they can nail the programs," said Hewlett Askew of the National Legal Aid and Defender Association, which has been an active opponent of administration legal-services policies.

Charles Jarvis, the new vice president of the Legal Services Corp., which provides funding for the individual programs, said the audits are required by Congress and are intended to improve those programs.

"We're primarily interested in excellence in serving the poor," he said. Jarvis added that the complaints have been generated because program administrators have gotten used to the "careless" auditing process that went on under previous administrations.

He said individual program officials resent the new "professional" audit approach. The old auditing system "bordered on charade . . . It's a major departure from past procedure."

"We've discovered in recent months that Legal Services appears to have fallen into the Defense Department trap in its monitoring . . . . It was a major problem. The monitoring was not done very carefully. There were cases where programs were asked to write their own monitoring reports . . . . " he said.

"We've entered a whole new stage . . . ," Jarvis said. "We want to identify weaknesses, make them aware that they may be transgressing statutes."

After he took office in 1981, President Reagan tried several times to abolish the Legal Services Corp., which distributes $305 million in federal funding to 325 legal-aid offices across the country.

Congress refused to abolish the program and enacted legislation forbidding cuts in funding to an individual program until the administration moved a board of directors through the Senate confirmation process. That board was finally confirmed late last year and a new president, John Wentzel, was put in place last summer. The auditing teams were quickly put into action.

The most recent protest has come from the San Francisco-based California Rural Legal Assistance (CRLA) where a group of 17 investigators spent two weeks last month. Jose R. Padilla, executive director of the program, recently protested to Wentzel that the audit team "was on a fishing expedition and that it intended to find fault regardless of the facts."

Texas Rural Legal Assistance, which is being audited, said that its monitoring team included a former Immigration and Naturalization Service official who is a former defendant in a lawsuit brought by the program charging abuse of foreign agricultural workers. Legal Services officials confirmed that charge, but said that, in that case, and in others, the use of teams of auditors prevents any one person from exerting undue influence on the process.

Lawyers at TRLA have also complained that the auditors have asked for copies of some 20,000 documents, which must be screened for client confidentiality, a project that will take at least a year.

At the Maryland Legal Aid Bureau, director Charles Dorsey refused last July to allow the auditors to review documents including confidential client files. After the auditing team was turned away, the corporation announced that it would suspend the program's funding. The Legal Aid Bureau filed suit in federal court and obtained an injunction barring a funding cutoff.

Major complaints in several of the audits have come after demands by monitors to review confidential client files. The American Bar Association said in an opinion that the programs should not reveal client names or any other confidential information that would tend to identify the client. Many state bar codes of conduct also forbid such disclosure.

"No one objects to giving them files with the names crossed out," Askew said. "That's enough information for them to check on the quality of representation . . . but they're not satisfied with that."

Jarvis said he believes the corporation has the right and often the obligation to go through all program documents, including client files, to make sure that "actual poor people are being served effectively."

He said it is sometimes necessary to see a specific file, especially in cases where the corporation is checking complaints made by clients against the individual programs. Besides, he added, "programs serving the poor should invite openness."

Another complaint has been that the auditors have no experience in poverty law. Of the CRLA audit, Padilla said, "At best, their backgrounds are simply irrelevant to the monitoring process. At worst, they have backgrounds reflecting strong antipathies to the rural poor," he said.

In that case, the auditing team was headed by James Norell, a former lobbyist for the National Rifle Association, and included a retired executive of the American Farm Bureau, a longtime opponent of Padilla's program, which has often brought lawsuits on behalf of migrant farm workers.

Others had backgrounds in criminal investigation, public relations and international law.

Askew said that a group of about 40 to 50 people, many of them "hostile" to legal services, make up the core of the monitoring teams. He said they are moving from program to program to lead the audits.

"Not a single one has ever worked in legal services, been on a legal-services board or taken a pro bono case," he said. "Their view is that this is one big national conspiracy. People who have been previously associated with legal services are considered tainted and can't be used."

Jarvis said he has chosen "people specially trained in auditing . . . people with decades of experience in analysis of federal programs."

Asked about complaints that the monitors are biased against legal services, Jarvis said each member of the team reaches his own conclusions, and "no one person can skew a report."