U.S. customs officials have detained since Tuesday an Ecuadoran jet cargo plane carrying military equipment, including Israeli-manufactured munitions, at New York's John F. Kennedy International Airport.

Officials at the State Department said there was no reason to believe the arms were bound for Argentina. The Ecuadoran airline and Israel denied any such intent.

The Boeing 707, which belongs to the state-owned Ecuatoriana Airlines, was described as "packed with cargo that included engine parts, bombs and bomb racks," according to informed government sources.

It landed in New York without an in-transit license, required under American law when an aircraft is carrying articles found on a munitions list maintained by the State Department.

The Ecuadoran Embassy filed an application yesterday for such a license, according to a department official.

There have been a flurry of rumors recently about Argentine attempts to purchase needed military equipment in various parts of the world. A source in London yesterday said the detained plane at JFK was destined for Argentina. On Tuesday, a dispatch from South Africa reported arms from that country were being sent aboard a Uruguayan transport plane marked as tractor parts. South Africa later denied the report.

The materiel aboard the Ecuadoran plane, according to Gustavo Izurieta, Miami general manager of Ecuatoriana Airlines, was "destined for the Ecuadoran Air Force."

A Washington source said yesterday the material appeared to be associated with a recent Ecuadoran purchase of six Israeli-built fighter planes.

The cargo plane, according to Izurieta, had been overhauled in Israel under a contract between the Ecuadoran Air Force and Israel Aircraft Industries, Ltd. The Ecuadorans were taking advantage of the flight back to Ecuador to bring aviation spare parts and logistical materials," Izurieta said.

The 707 flew into JFK Tuesday morning for refueling after an intervening stop at Shannon, Ireland, according to Izurieta. While at the New York airport, it was subjected to a spot customs check under "Operation Exodus," the Reagan administration's program to prevent the unauthorized export of technical equipment of military value to the Soviet Bloc or Third World countries.

Officials said inspectors found the cargo did not reflect what was on the plane's manifest, which reportedly referred only to engine spare parts.

Washington Post correspondent William Claiborne reported from Jerusalem that Israeli Foreign Ministry officials told British Ambassador Patrick Moberly there was no basis for reports that the plane was destined for Argentina.

Israeli officials said Israel has no intention of interfering in the British-Argentine conflict and that no new arms contracts have been signed since the Falklands crisis erupted.