Two civil rights organizations yesterday rebutted the Reagan administration's finding that El Salvador is entitled to continue receiving U.S. military aid.

In the latest volley over the situtation in El Salvador, the American Civil Liberties Union and the Americas Watch Committee charged that the State Department's certification report earlier this week contained "sufficient evidence to make clear that the conditions for certification have not been met."

The groups added that their 272-page report on El Salvador, issued this month, refuted the department's findings.

In order to continue military aid and arms sales to El Salvador, the administration is required by law to certify that the country is making progress in human rights, disciplining its armed forces and promoting economic and political reforms.

Among the points made in the groups' rebuttal:

* While the State Department report said that political violence in El Salvador has declined in the last six months, "there is simply no basis for concluding that the actual numbers of political murders" there have dropped.

The lower numbers, they said, are due in part to the Salvadoran security forces' new tactic of hiding bodies rather than leaving them in plain view as a warning to others, and a shift in political violence to more rural areas not covered by human-rights monitors and the press.

* The State Department report cited as evidence of the Salvadoran government's "demonstrable attempt" to control its forces the arrests of 47 military and at least 10 civil defense personnel on charges of murder, assault and other crimes since Jan. 1.

The groups noted, however, that "none of the cases submitted to the civilian judiciary has yet been brought to trial."

* The State Department report stressed that Defense Minister Gen. Jose Guillermo Garcia ordered Salvadoran security forces to respect human rights.

But, the groups said, "there is no reason to believe that this instruction will be any more effective" than a code of conduct issued in January under which soldiers pledged to respect human rights.

The Reagan administration, the groups charged, "relies on empty promises rather than actual performance."

The groups are to testify before the Senate Foreign Relations Committee next week.