The Merit Systems Protection Board and its office of special counsel cut their fiscal 1982 budgets in such a way that it cost the federal government more money and significantly weakened protections for whistle blowers and other civil servants, the General Accounting Office has concluded in a new report.

In one case, the board forced an unidentified federal agency to pay more than $6,000 to send 23 witnesses to a hearing in Dallas rather than spend $325 to send one MSPB hearing officer out of town.

Like many other federal agencies, the merit board was caught in a squabble between the White House and Congress last year. It resulted in a 16 percent budget cut for the agency.

The cuts hit the merit board particularly hard, the GAO report (GAO/FPCD-83-20) said, because they coincided with the filing of 10,700 appeals by air traffic controllers fired by the Reagan administration.

Because the board's staff was willing to put in "a large amount of uncompensated overtime," it prevented operations from "coming to a complete stop," the GAO said.

The budget crunch forced the board to hold all hearings at its 11 regional offices rather in the field. The move saved the board money, but proved costly to other agencies, the report said.

At least 400 cases had to be postponed because of cuts in travel funds, including nearly all cases filed by employes in Alaska, Panama, the Far East and Europe.

The GAO's harshest criticism was aimed at the special counsel's office, which is responsible for protecting federal workers. It said the office, under then-special counsel Alex Kozinski, enacted policies that seemed more restrictive than necessary to meet the budget.

In particular, the GAO said Kozinski ordered managers to reduce the number of complaints that had been pending at least nine months. Within four months, the number of pending cases dropped from 350 to 100 as managers closed cases in "assembly-line fashion" with only cursory review, the GAO said. "Many potentially valid cases were closed prematurely," according to the GAO.

What made such restrictions suspect, the GAO said, was that more than half of the office's travel funds during the first nine months of the fiscal year were spent by managers to attend training courses, including a Washington seminar on how managers could lay off employes legally.

Although the merit board admitted that the GAO study was "factually correct," it said it has modified its travel policy so that hearings are now held at the most economical location. The special counsel's office declined to comment.