WASHINGTON, June 21.-A freighter flying the flag of Pakistan was preparing today to sail from New York for Karachi with a cargo of United States military equipment for Pakistan, apparently in violation of the Administration's officially proclaimed ban on such shipments.

Senior State Department officials, in response to inquiries, acknowledged that at least one other ship was now on the way from the United States to Pakistan carrying what they described as "foreign military sales" items.

These items, they indicated, came from excess Defense Department stocks and apparently were shipped as a result of confusion within the Administration as to how the three-month-old ban on shipments of military equipment to Pakistan should be applied.

"There has evidently been some kind of slippage here," an official said.

TO KARACHI IN AUGUST

The Padma, the ship that was preparing to sail from New York, is scheduled to arrive in Karachi in mid-August with a cargo that is said to include eight aircraft, parachutes and hundreds of thousands of pounds of spare parts and accessories for planes and military vehicles .

The Sunderbans, another ship of Pakistani registry, sailed from New York on May 8 with other items of military equipment for Pakistan including parts for armored personnel carriers, according to the ship's manifesto and the accompanying State Department export license. She is due to arrive in Karachi Wednesday. All this equipment has been sold to Pakistan by the United States Air Force under provisions of the Foreign Military Sales Act.

After troops of the Pakistani Army, mainly West Pakistanis, were ordered to crush the self-rule movements in East Pakistan last March 25, the State Department announced that all sales of military equipment to Pakistan had been suspended and that the program, initiated in 1967, had been placed "under review."

Today, State Department officials, responding to queries about the sailings of the Padma and the Sunderbans, said that it remained the official policy of the Administration that sales of all types of military equipment to Pakistan were prohibited under the ban imposed shortly after the severe repression of the East Pakistani independence movement began early in the spring. The State Department estimates that at least 200,000 East Pakistanis have died in the subsequent fighting and that about six million refugees have fled to India.

Senior State Department officials said in interviews today that they were not aware of shipments of military equipment to Pakistan after March 25.

They acknowledged that such shipments would constitute a violation of the proclaimed policy.

The State Department officials said they had been informed by the Defense Department that no military equipment under the foreign sales program had been delivered "to the Government of Pakistan or agents of the Government of Pakistan" since March 25.

NO EXPLANATION OFFERED

They said the Defense Department "reaffirmed" this policy today in discussions with the State Department. They could not explain how this Pentagon statement could be reconciled with the fact that, according to the bills of lading submitted to the Pakistani Embassy here, the equipment to be loaded on the Sunderbans was received at the dock in New York on April 23 and the equipment for the Padma on May 21.

A communication from the shippers to Lieut. Col. M. Akram Raja at the defense procurement division of the Pakistani Embassy covering the dock receipts for the two ships was sent on May 21.

The Defense Department, asked about the shipments last Saturday and again today, referred all inquiries to the State Department. Officials appeared to be at a loss for an explanation of the shipments.

State Department sources quoted the Defense Department as saying that no sales or deliveries to Pakistan had been authorized since March 25 and that the equipment aboard the two freighters had been purchased prior to the official prohibition.

INQUIRY BY SENATOR CHURCH

But they offered no comment as to why the dockside deliveries and actual shipments had been made after March 25.

The State Department has not yet replied to a letter sent on June 17, by Senator Frank Church, Democrat of Idaho, to Secretary of State William P. Rogers requesting information about "certain items of military equipment" being shipped to Pakistan under State Department licenses.

Senator Church who is a member of the Senate Foreign Relations Committee, advised Mr. Rogers that he understood that the State Department had issued License No. 19242 for some of this equipment.

A check of the bills of lading of the cargo aboard the Sunderbans showed that this license covered an item described as "28 skids, parts," weighing 11,895 pounds. No further description of these items was available.

But another license issued by the State Department for the Sunderban's cargo specified "parts and accessories for military vehicles." The Sunderbans carries a total of 21 items, according to the dockside delivery listings, identified on these documents only as cases and Cartons of "auto parts and accessories," "skids and parts," "boxes" and "parts"

PLANES AND PARACHUTES LISTED

The dockside delivery listings for the Padma include two entries of "four aircraft" each, 113 parachutes and parts, and auto parts, accessories, skids and wooden boxes."

An item described as "crates, bundles and parts" is listed as weighing 14,133 pounds.

The program of military sales to Pakistan, begun in 1967, had been running at nearly S10-million a year, according to Robert J. McCloskey, the State Department spokesman. The United States agreed in that year to sell non-lethal" equipment to both Pakistan and India, lifting of part the embargo placed on military deliveries after the 1965 Indian-Pakistani war.

In October, 1970, the Administration agreed, as an "exception," to sell Pakistan an undisclosed number of F-104 fighter planes, B-57 bombers, and armored personnel carriers. However, the State Department said today that none of this "exception" equipment had been delivered.

But authoritative sources here, who cannot be identified, said that the flow of military equipment to Pakistan from Air Force sales alone had reached $47,944,781 between 1967 and April 30, 1970.

A communication sent on May 28 to the defense procurement division of the Pakistani Embassy by the headquarters of the Air Force accounting and finance center in Denver enclosed a "status report . . . listing all your open foreign military sales cases, showing case value, amounts collected, delivered and undelivered."

The letter-signed by Elaine B. Loventhal chief foreign military sales branch comptroller at the Denver headquarters-was headed: "USAF statement of military sales transactions and detail delivery listings."

The "status report" noted that previous charges on Pakistani military purchases were S25,679,654.10, that undelivered items totaled S21,730,740.07 and that "cash received to date" was $24,342,782.37.

State Department officials were unable to say precisely what period this report covered.

The Air Force report said, however, that the Pakistani Government had to remit "on or before 31 May, 1971" the sum of S3,376,253.51 for further "total cash requirements."

A notation on the report showed that a check from Pakistan for S404,116.49 had been received "in May, 1971."

Authoritative sources here said that "in all likelihood" additional sales to Pakistan might have been made by the Army and the Navy.

Spokesmen for the East West Shipping Agency, the New York agents for the Padma and the Sunderbans, indicated that the Padma had carried military equipment to Pakistan on a number of recent voyages, most recently delivering it in Karachi on March 22, three days before the troop action in East Pakistan.

The voyage for which the Padma is now preparing is her first to Karachi carrying military equipment since the ban was imposed after March 25. The current trip by the Sunderbans is also her first with such equipment since the ban. But authoritative sources said that other ships with military equipment for Pakistan might have sailed since March 25 from East and West Coast ports .