A federal judge turned aside an 11th-hour move yesterday by two labor unions to prevent the federal government from instituting controversial changes in rules governing pay raises, layoffs and other personnel practices for government employes.

Judge Thomas Penfield Jackson said he would allow the Office of Personnel Management to put the revised regulations into effect Monday because he did not believe there was any immediate prospect of firings or other major actions against federal workers.

Any disputes stemming from the new rules may be settled later in Congress, in court or through other proceedings, the U.S. District Court judge said.

Lawyers for the American Federation of Government Employees, which claims to represent 700,000 federal workers, immediately appealed Jackson's ruling to the U.S. Court of Appeals here. The union asked the appellate court to block the new rules from taking effect.

Robert Tobias, president of the 110,000-member National Treasury Employees Union, denounced Jackson's ruling, contending it will lead to widespread disruption in personnel proceedings.

The revised regulations were drawn up by the Reagan administration in an attempt to put more emphasis on federal workers' performance and less on seniority. The rules are expected to make it more difficult for employes to gain regular pay increases and to weaken job security for longtime employes.

The shift would affect the way longevity pay raises and reductions in force are carried out for 1.2 million white-collar government workers, including about 360,000 in the Washington and Baltimore areas.

Congress has twice barred the Office of Personnel Management from instituting the revamped regulations. But the latest congressional ban will expire Monday. With Congress in recess, no further action is likely before mid-July, officials said.

An amendment to delay the shift in rules, sponsored by Rep. Steny H. Hoyer (D-Md.), has been approved by the House as part of an appropriations measure. No similar provision has been adopted by the Senate. A House-Senate conference committee is expected to decide soon whether to retain the Hoyer amendment.

Earlier this week, the Office of Personnel Management indicated it might withdraw the proposed rules, but the OPM move was quickly overturned by the Office of Management and Budget. An OMB spokesman said the proposed delay was rejected because the new rules reflected administration policy.

In a further sign of last-minute jockeying, Rep. Frank R. Wolf (R-Va.) called on OMB director David A. Stockman to "pull back" the revised rules. "The people who are threatened by these regulations are loyal, dependable, fully successful performing civil servants," Wolf said in a letter released yesterday.

In his ruling yesterday, Jackson chided the unions for delaying their court challenge until three days before the rules were due to take effect, and he said that Congress should not expect the courts to "relieve it of the time pressure" of Monday's deadline by interceding in the personnel dispute.