Congress enacted the District of Columbia's $1.3 billion operating budget for the 1979 fiscal year yesterday with separate votes in the House and Senate.

The votes of 339 to 31 in the House and 76 to 8 in the Senate sent the measure to President Carter for his signature. For the fiscal year, which starts Oct. 1, Congress approved a $235 million federal payment as the U.S. share of city costs, $82 million less than the president had requested.

In approving the budget, both chambers adopted a report that scolded the D.C. government for what the Lawmakers called "the city's excessively large payroll," and called upon officials to take steps to reduce it.

The city has 38,000 employes paid from congressionally appropriated funds, and about 7,000 others paid from federal grants.

In the report, the lawmaker said the District had 730 employes for each 10,000 of population in 1974-75, or about 45 percent above the national average. City officials have described such comparisons as unfair, saying Washington is the only totally urbanized governmental unit in the country combining state, county and municipal functions.

The final budget eliminates $275,000 previously approved by the Senate for improvements at the city dog pound. It will provide $625,000 to operate the city's Advisory neighborhood Commissions in the coming fiscal year, halfway between the original House and Senate figures.

Both houses agreed to cut $10 million from the police and firefighters' pension fund in an attempt to pressure the city to tighten disability retirement provisions. Pension payments to current retirees will not be affected.