President Reagan will seek an additional $400 million in economic and military aid for Central America next year in a sharply stepped-up effort to reconstruct the region and contain leftist insurgency there, a senior administration official said yesterday.

He said the Office of Management and Budget already is drawing up proposals for the increase, which would include an additional $300 million in assistance for health systems, political change and economic development and another $100 million in military aid to U.S.-backed governments in El Salvador and elsewhere in Central America. This would nearly double the present level of economic aid and increase the military budget for the region by 40 percent.

The disclosure came on a day when House and Senate conferees gave the administration $25 million more in military aid for El Salvador, splitting their differences and leaving Reagan with a total of only about half the $110 million in additional aid he had requested.

White House spokesman Larry Speakes said of this decision that "we don't like it at all," but other officials said the administration could easily live with the compromise, at least until the newly named National Bipartisan Commission on Central America, headed by former secretary of state Henry A. Kissinger, reports to Reagan on Dec. 1.

The senior official who disclosed the new economic proposal for Central America said the administration was drawing up its budget proposals in expectation that the Kissinger commission would recommend major increases in economic outlays.

Meanwhile, Secretary of State George P. Shultz told Congress yesterday that the government of El Salvador continues to make enough progress in human rights to qualify for military aid, although he added that its "record falls short of the broad and sustained progress" the administration would like to see.

The certification comes despite an increase in the number of civilians killed by all sides in that country during the last six months.

Official U.S. Embassy figures show that 1,054 civilians were killed in the first six months of 1983, compared with 961 during the last half of 1982. Information collected by the Roman Catholic Church in El Salvador puts the death total much higher--2,527 slayings in the first six months of this year, compared with 2,340 during the previous six months.

Congress has made human rights certification by the president a condition for continued military aid to the Salvadoran government.

The House had approved no increase in military aid for El Salvador in its version of the supplemental appropriations bill that came out of conference yesterday. The Senate had approved all $50 million Reagan requested. He also asked for permission to shift $60 million appropriated earlier for other countries. He received permission to shift $30 million.

A senior administration official said these split-the-difference decisions would eventually cause the Salvadoran government to "bleed to death" but acknowledged it would be sufficient to enable the government to continue its campaign against leftist insurgents for the balance of the year.

This official said that the action also underscored the importance of the Kissinger commission, which is expected to put Central America's problems more prominently in focus.

"It will be more difficult for the Democrats to dodge their responsibility once the dimensions of the problem are properly framed," an official said in reference to the commission.

Reagan announced yesterday that he is appointing Harry W. Schlaudeman, ambassador to Argentina, as executive director of the newly created commission. House Speaker Thomas P. (Tip) O'Neill Jr. (D-Mass.) announced he is appointing Majority Leader James C. Wright Jr. (D-Tex.) and Michael D. Barnes (D-Md.) as the two House Democrats who will be among the eight congressional counselors to the commission.

Wright generally has been supportive of Reagan administration policy in Central America, while Barnes has been an outspoken critic.

The administration submitted what amounted to a heavily qualified certification of "concerted and significant progress" toward curbing human rights abuses in El Salvador.

"It is evident that the record falls short of the broad and sustained progress which both the Congress and the administration believe is necessary for the evolution of a just and democratic society in El Salvador," Shultz wrote in a letter accompanying the certification and a report providing the reasoning and facts behind certification.

The report noted the rise in civilian deaths, the continuing inability of the government to identify and punish those in the military who abuse human rights and "uneven and disappointing" progress toward solving the murders of several American churchwomen.

But the report said those problems were counterbalanced by progress in other areas: the establishment of a Peace Commission to cajole the warring factions into scheduled elections later in the year, an amnesty program that has led to release of 500 political prisoners and the extension of the land-reform program.

A senior administration official acknowledged that "the record falls short of what it should be," but said it would be inappropriate to characterize the certification as "reluctant," preferring to call El Salvador's progress "disappointing."

"The fact that the secretary has found the government of El Salvador to be meeting these statutory standards is not to say that he is satisfied with the progress that has been made," the official said. "Indeed, the transmittal letter conveys a sense of disappointment that more progress has not been made."

But Sen. Patrick J. Leahy (D-Vt.) said he could not see how the administration could certify progress, given the evident lack of progress.

"There has been no progress in the nuns' case and civilian deaths have gone up," said Leahy. "If we can have certification under these circumstances, I cannot imagine how bad things would have to get before this administration would not certify that the conditions of the law had been met."

The senior official, speaking on condition that he not be identified, called the increase in civilian deaths "a serious problem," but said that the law requires certification that the Salvadoran government "is making a concerted and significant effort to comply with internationally recognized human rights, and is achieving substantial control over its armed forces."

"The statutory criteria are met," said the official. "This is a law that was written about El Salvador and not Utopia, and the effort is being made. The results are in some areas disappointing, and acutely disappointing, and require further intense efforts by the government of El Salvador. And, we think, El Salvador requires our support and assistance for those efforts."

The certification was the fourth and final one required of the administration every 180 days by legislation passed in 1981. Pending in both the House and Senate is legislation to extend and broaden the character of progress reports required of the administration in order to ensure a continued flow of military aid to El Salvador.