Twelve church and political organizations yesterday sharply challenged recent State Department reports on human rights conditions in five countries overseas, and asked President-elect Jimmy Carter to order that more and better information be made public.

The organizations also asked Carter to cut off U.S. security assistance to Argentina, Haiti, Indonesia, Iran and the Philippines on grounds that they engage in "a consistent pattern of gross violation of internationally recognized human rights." These countries, plus Peru, which the organizations did not mention, were the subject of State Department reports released Jan. 1, the first in a series of human rights studies required by Congress in a recent law.

In a private meeting with about 50 members of Congress last Wednesday at the Smithsonian Insitution, Carter praised the congressional requirement for an accounting of human rights conditions in countries receiving U.S. aid or arms. According to participants, the President-elect said the congressional action had prodluced positive results in a number of countries, including the release of political prisoners in several.

Carter placed stress on human rights aspects of U.S. foreign policy during his campaign, declaring his opposition to U.S. aid to repressive and dictatorial governments. He was minded of his campaign statements in a letter to him released yesterday by the 12 organizations which included Americans for Democratic Action, the Friends Committee on National Legislation, and the Jesuit Office of Social Ministries.

"The State Department figures gives for political prisoners [in its recent reports] are consistently underestimated and do not take into consideration higher estimates by international organizations. Responsible reports from international legal and human rights groups alleging widespread and routine torture by police and army personnel with the sanction of government leaders, are downgraded or disregarded entirely," the letter to Carter charged.

The organizations also said that U.S. security assistance to repressive governments gives them "an appearance of legitmacy." While U.S. aid may help achieve stability in the short run for individual leaders and groups, eventually "unpopular governments which use secret police, detention without charges and torture to maintain their power will fall," the organizations asserted.

The letter to Carter made no comment on the State Department claim in its reports that U.S. diplomats and military officials have been trying to convince foreign governments to improve civil liberties and police practices in their countries. However, an analysis of the State Department reports which accompanied the letter suggets that increases in U.S. aid to repressive governments have undercut the diplomatic advice.

President Ferdinand E. Marcos of the Philippines has taken strong exception to the State Department human rights report on his country, calling it a "particularly offensive document" and threatening to break military ties with the United States. Marcos' government is negotiating with the United States over continued use of major military bases at Clark Field and Subic bay.

The organization that wrote to Carter urged him to stand firm on human rights in the Philippines and reduce military aid there regardless of that government's decision on the U.S. bases.

"There is no longer a clear case in the post-Vietnam era for a forward deployment in the Pacific that requires the continuation of the bases," the letter maintained.