House Democrats sharply criticized President Reagan yesterday for certifying improvement in the human rights record in El Salvador but admitted they doubt that they can block his new military aid program for that country.

They charge that the president's account of declining political killings does not square with reports of independent human rights organizations, which have found continuing high levels of slayings, torture, and abductions in El Salvador.

Peppered with questions by Democrats, Assistant Secretary of State Thomas O. Enders supported Reagan's position. He told a House Foreign Affairs subcommittee that although slayings continue, the "trend is downwards."

Reagan last week formally certified to Congress an improvement in human rights in El Salvador and asserted that the military-civilian junta running the country is achieving more control over military forces, which frequently are accused of slaying civilians. Both assertions were required by the Foreign Aid Act under which the administration will supply the junta with $26 million in military assistance this year. Reagan is sending an additional $55 million from a Pentagon fund that is unrestricted.

House Democrats launched two offensives to block the aid. Reps. Gerry E. Studds of Massachusetts, Tom Harkin of Iowa and Bob Edgar of Pennsylvania and about 30 other members introduced a bill to cut off aid and declare the presidential certification void. Even if the measure passed both Houses, Reagan could veto it and it is doubtful a veto could be overridden.

Studds said the purpose of the bill is "to make it as costly as possible in political terms for the administration to proceed on this course."

In addition, more than 50 House members, most of them Democrats, sent Reagan a letter asking him to withdraw the certification because it "is contrary to the documented facts."

Rep. Michael D. Barnes (D-Md.), whose House Foreign Affairs subcommittee began three days of hearings on El Salvador, charged that by certifying an improved human rights record in the face of two episodes involving civilian deaths, the administration sent the wrong signal to the Salvadoran government. He said it would undercut that government's effort to control the military.