An administrative law judge has criticized the Merit Systems Protection Board's Office of Special Counsel for filing a charge against a federal employe that was "clearly without merit" and has ordered it to pay the employe's legal fees.

The ruling is believed to be the first time the special counsel's office has been ordered to pay a defendant's legal fees.

It comes as the office is trying to shed the politically partisan image it developed under former special counsel Alex Kozinski, who brought the case.

Alan W. Heifetz, the Housing and Urban Development Department judge to whom the case was referred, gave the special counsel's office until February to appeal the ruling or pay $5,369 in legal expenses incurred last year by Guadalupe Saldana, an Environmental Protection Agency employe.

K. William O'Connor, who succeeded Kozinski, is reviewing the case.

Last June, Kozinski accused Saldana of violating the Hatch Act, which limits partisan political activity by federal employes, by endorsing President Carter for reelection during a White House news conference in March, 1980. Saldana, then president of the American GI Forum, a national Hispanic organization, had been called to the White House to discuss Hispanic-related issues.

Saldana said he was asked before the meeting with Carter if he would endorse the president, but he refused because his organization does not make endorsements. After the meeting, some of the Hispanic leaders in attendance endorsed Carter, but Saldana said he did not.

According to testimony, the office decided to investigate Saldana based on media accounts of the news conference. But the judge said the office made no attempt to check the accuracy of the stories, ignored key witnesses who had attended the meeting and news conference and whose testimony supported Saldana, and pursued the case even though it turned up no evidence that Saldana had broken the law.

"In the absence of any reliable, probative or competent evidence, . . . the charge was hurled at him Saldana on the witness stand to deny. The argument was then made that the denial, because it was not to be believed, was enough to sustain the charge," Heifetz said. "This is not a failure to produce a preponderance of evidence; the failure is to produce any evidence."

Heifetz said there was "nothing in the record" that showed federal prosecutors had "intentionally harassed" Saldana. "The result came more from accident than design."

However, Saldana yesterday said he believes the office singled him out because he is Hispanic and because they wanted to punish Hispanics for not supporting Reagan. Saldana testified at his hearing that he had been denied a promotion from his current GS-14 level to a GS-15 while the charges were pending against him.

During 12 of his 14 months in office, Kozinski filed five Hatch Act cases, all against Democrats, according to the office's annual report. He would not comment yesterday on the Saldana case.

The MSPB is reviewing 16 Hatch Act cases, an aide to O'Connor said, nine cases involving Democrats and seven involving Republicans. They were filed either by Kozinski or his predecessors, she said.

O'Connor said yesterday he doesn't feel that Hatch Act cases should be a priority for the office, which was created primarily to protect federal whistle blowers.