U.S. intelligence agencies believes about 90 percent of the American hostages are locked up in the Tehran embassy but are not sure of the whereabouts of the other 10 percent, government officials said yesterday.

This uncertinty frustrates the Joint Chiefs of Staff as they continue to look for ways to rescue the 52 hostages by military force without suffering unacceptably high casualties.

The Pentagon kept studying rescue plans after the April attempt ended in flames on an expanse of sand in the Iranian back country called Desert One. But, Pentagon sources said, lack of precise intelligence on all the hostages" location made trying to find and extract them in a lightning-fast night operation too risky.

Intelligence analysts never believed the hostages were widely scattered thrroughout Iran after the April raid, as the Iranian government claimed. They still think the hostages are in Tehran, with the 10 percent outside the embassy suspected to be elsewhere in the city.

But nobody pretends to have unimpeachable information about what is going on inside Iran these days, partly because the CIA's network there disintegrated along with the shah's power in 1968. The unsuccessful April raid, code-named Rice Bowl to steer people away from the location if word about it leaked out, tore up what was left of the CIA's once-elabrate network in Iran.

The intelligence gap extends beyond the hostages' location to the war between Iran and Iraq. Estimates about its direction by the CIA and Defense Intelligence Agency have proved wrong.

Early in the war, the CIA issued dire secret reports about the possibility that the Strait of Hormuz in the Persian Gulf could be closed to oil tankers by one of the combatants. The DIA kept saying the war would sputter out in a matter of days, citing the likehood that Iran would run out of fuel for its warplanes as one reason for this.

The CIA moderated its warinings when the U.S. Maritime Administration, after checking with companies whose ships were plying the Persian Gulf, reported business as usual except for some challenges from the Iranian navy.

The duration and tempo of the of the Iranian-Iraqi war exceeded DIA's early predictions, Pentagon officials acknowledge. However, they said there has been a slowdown lately in Iran's air operations.

Despite the high risk, the president could always order another attempt to free the hostages by force if it seemed the only way to get at least some of them out alive. But for some time the post-April rescue plans have been consigned to the Pentagon's bottom drawer, sources said.

Columnist Jack Anderson wrote in August that President Carter had given the go-ahead for an invasion of Iran in mid-October, asserting that the Kharg Island oil terminal at the head of the Persian Gulf was an objective. Rescue plans hve focused on direct extraction of the hostages, Pentagon sources said, not the occupation of Kharg Island or the oil fields.

Before the April attempt was launched, former CIA director Richard Helms was one of those pushing for a U.S. military occupation of Kharg Island so iran's oil spigot there could be controlled by the United States, sources said. However, the Kharg Island occupation was approved then or later.

With military rescue out at least for the moment, the government's intelligence agencies are trying to find out what discussions are going on behind closed doors in Iran's ruling circles concerning the hostages. But here, too, gathering hard information by such standard techniques as electronic eavesdropping is proving difficult.

One reason for this is that the Ayatollah Ruhollah Khomeini and his top aides do not communicate much beyond their tight circle, keeping Washington and other world capitals pretty much in the dark about their plans.