WASHINGTON.-The Nixon Administration discovered from newspaper disclosures last week that it has been violating the ban it had imposed on shipments of American military equipment to Pakistan following the outbreak of civil strife in that country's eastern region.

In finding out belatedly that at least three freighters laden with military equipment had sailed from New York for Karachi after the ban became effective on March 25, and that new export licenses had been illegally issued since that date, the Administration faced public embarrassment, Senatorial anger and political problems with India.

The incident also served to underscore Washington's ambiguous attitude toward the potentially explosive situation In East Pakistan, where Pakistan's military suppression of the Bengali independence movement is reported to have claimed nearly 200,000 Bengali lives and has sent six million refugees pouring across the Indian border.

Few observers believed that any deliberate official deception was involved. It was generally accepted that the arms shipments resulted from a breakdown in internal communications between those who make policy at the top and those executing it on the working level, a phenomenon that one harried bureaucrat described last week as "the price you pay for an elephantine government."

The bureaucratic confusion surrounding the shipments was monumental in every aspect. The State Department, which had assured a number of Senators only a few weeks earlier (in writing) that no arms shipments to Pakistan were scheduled, was surprised to learn of the sailing of two freighters (it later discovered the third one) and turned to the Defense Department for explanation.

The Pentagon checked its computers and produced the information, startling the State Department, that the March 25 ban on shipments took effect only on April 6. Then, the Administration explained that military equipment delivered to Pakistani officials In the United States before March 25 could be shipped anyway. It did not say why.

A special high-level task force was quickly formed to ascertain the facts, but four days elapsed before the State Department learned that the Padma, the Pakistani freighter loading in New York last weekend, had sailed with (1) S1.2-million worth of ammunition, (2) spare parts for military aircraft, armored vehicles and Jeeps and (3) small radio-controlled pilotless drones for antiaircraft gunners' practice.

For three days, State Department spokesmen and newsmen argued over the official claim that ammunition was not a "lethal" item. This stemmed from an earlier State Department admission that the military sales to Pakistan, confined to "non-lethal" items included ammunition. On the third day, a reporter asked: "When does ammunition become lethal?" The State Department spokesman replied: "This is a theological question." Left unclear was the essence of United States policy toward the East Pakistani crisis against the background of what is recognized here as a very real threat of warfare between India and Pakistan unless a political solution is promptly found for the autonomy aspirations of the easterners.

This threat emanates from the severe strain that the refugee army has placed on India's resources, the mounting frictions between the refugees and the local Indian population and India's fear of political radicalization of the East Pakistan "freedom fighters."

All these factors are seen by New Delhi as a direct menace to the political stability of the Indian state of West Bengal and to peace in the subcontinent Indian policy, strongly supported by Britain and Canada, is to bring enough international pressure to bear on President Yahya Khan to grant East Pakistan its demands for autonomy. India argues that this must be done if conditions are to be restored in East Pakistan for the return of the refugees. She insists that foreign economic aid must be denied Pakistan as an instrument of pressure.

The attitude of the United States on this point is ambiguous. The Administration's instincts, particularly at the Pentagon, are that reasonably good relations with Pakistan must be maintained at all costs so as to compensate for the close ties between India and the Soviet Union. This view is maintained even though Pakistan in recent years has drawn close to Communist China.

Although the State Department publicly counseled Pakistan earlier this month to seek "political accommodation" with the easterners-the first time it had done so after two months of bloody fighting-it rejects the argument that economic pressure should be applied .

However, a mission from the World Bank recommended last week. following a survey of the Pakistani situation, that no new funds be supplied by the International aid- to-Pakistan consortium until the Islamabad regime had turned to "political accommodation" in the East.