President Reagan told Congress yesterday that the El Salvador government's human rights record entitles it to receive U.S. aid, and the State Department said it is urgently studying the need to increase assistance to the regime there following an attack by leftist guerrillas Wednesday on the country's main military air base.

These actions set the stage for a potentially major new battle between the administration and congressional liberals, who contend that the military-civilian regime headed by President Jose Napoleon Duarte continues to sytematically violate human rights.

Reagan's declaration, in the form of a certification to Congress, clears the way for the administration to disburse $26 million in military assistance allotted for El Salvador under the fiscal 1982 foreign aid bill. In passing the legislation last month, Congress attached a provision requiring the president to certify that the Salvadoran government was ending rights abuses and making progress toward political and economic reform.

In his certification, Reagan concluded that the Duarte regime "has made a concerted, significant and good-faith effort to deal with the complex political, social and human rights problems it is confronting and that progress is being made."

But, the president's contention came in a week that saw the American Civil Liberties Union and other human rights groups accuse Salvadoran authorities of continuing repression--including allegedly being responsible for the murder of 12,501 persons during 1981. Also this week, The Washington Post and the New York Times published reports from El Salvador quoting witnesses who charged government forces with a large-scale massacre last month in the rural Morazan province.

The wide disparity between these charges and the administration's defense of the regime seems certain to trigger new efforts by human-rights advocates in Congress to cut off or place new restrictions on U.S. military aid.

The confrontation is likely to be hastened by the success of Cuban-backed guerrillas in damaging or destroying several helicopters and planes in Wednesday's bombing attack at the Ilopango air base near San Salvador.

State Department spokesman Alan Romberg yesterday called the attack an attempt by the guerrillas to disrupt the elections for a constituent assembly scheduled for March and added:

"We cannot allow terrorists committed to achieving power through violence and the destruction of the country's economic infrastructure to undermine these efforts. Accordingly, we must be prepared to increase our economic and our military assistance to El Salvador as necessary. We are presently reassessing assistance needs on an urgent basis."

Romberg refused to spell out what a request for additional aid might entail.

However, congressional sources said the Senate Foreign Relations Committee yesterday was given a secret intelligence briefing at which administration officials admitted that the Salvadoran military's ability to support ground operations against the guerrillas had been sharply impaired and possibly eliminated.

The sources speculated that the administration, at a minimum, will seek to replace the heavy-duty Huey helicopters that were lost in Wednesday's bombing attack.

However, two members of Congress, Democrats Reps. Tom Harkin (Iowa) and Gerry E. Studds (Mass.), served notice that they will introduce legislation next week to cut off all military aid, and they are expected to be joined by other congressional liberals who successfully got the presidential certification requirement into the foreign aid legislation.

State Department officials said Reagan's rationale for the certification will be described in detail when administration officials testify Monday and Tuesday before the Senate and House subcommittees on inter-American affairs.

In the message sent to Congress yesterday, the president briefly explained his reasoning.

Essentially, he said that, while some abuses continue in the difficult circumstances imposed by civil war, the Duarte government is making a sincere effort "to comply with internationally recognized human rights" and "is achieving substantial control" over the armed forces through such measures as outlawing extremist paramilitary groups and imposing a code of conduct on the military.

Reagan contended these efforts are "beginning to have a positive effect" and have produced "a declining level of violence over the past year."

The president also certified that the Salvadoran government is working hard to solve the 1980 murders of four American Roman Catholic women missionaries and "has uncovered additional evidence which gives hope of substantial new progress." He also said the government has been "pursuing in good faith" its investigation of the murders of two American agrarian reform advisers.