As fighting between Iran and Iraq entered its fifth day, administration officials said yesterday Iraqi intentions appear aimed at fighting a limited, rather than all-out, war, with Baghdad's main goal being the control of the disputed Shatt-al-Arab waterway and border regions to the north.

At the same time, some senior specialists believe the Baghdad government is also looking for a possible "bonus" from its thrust into Iran and occupation of Iranian territory -- the toppling from power of Ayatollah Ruhollah Khomeini.

Longstanding and deep-rooted fear in the Iraqi government of Khomeini, who has frequently called on Iraq's sizable Shiite Moslem population to overthrow the "satanic" government of the ruling Baath Party, is viewed by many intelligence officials as a factor that led Iraq to launch its incursion into Iran now, a time of Iranian military weakness.

If it turns out that Iran is unable to oust Iraqi forces from territory they now hold inside Iran, and more that they still might grab, then some specialists believe this ultimately could be enough of a humiliation to unravel Khomeini's power and that this figures in Iraqi calculations. Others argue that defeat in a border war would not necessarily hurt Khomeini.

Iraq's main territorial aims involve regaining complete sovereignty over the waterway leading into the Persian Gulf, thereby ending a 1975 agreement with the late shah of Iran that set the border in the middle of the river. Also, Iraq seeks sovereignty over disputed lands to the north of the estuary and reestablishment of "Arab" sovereignty over three small islands in the Persian Gulf.

In addition, analysts here say Iraq may try and expand its foothold in Iran further east, taking additional territory as a buffer zone and potential bargaining chip that they could give up in any future negotiations meant to ensure their control over the waterway region.

U.S. officials say that thus far the Iraqis seem to be carrying out their strategy "rather well." But the question of how far to thrust into Iran is the most delicate and dangerous.

It could produce chaos in Iran if it goes too far, they believe, possibly setting off turbulence in provincial areas elsewhere in Iran which could give the Soviet Union, with strong forces to the north, a pretext for entering Iran. Or, it could provoke the Iranians to "bring down the house with them"

U.S. policymakers admit that their assessment of Iraqi intentions is based on deduction and educated guesses. But they clearly are hopeful that Iraq, which appears to have the upper hand militarily, will be content with achieving its limited territorial goals and that within a few days both sides might be at a point where they would welcome an opportunity to wind down the fighting.

For that reason, the main thrust of U.S. policy is to encourage efforts -- either in the framework of the United Nations or through an initiative by the Islamic bloc of countries -- that will give Iraq and Iran the chance to accept a cease-fire and mediation of their dispute.

"It's still a wide-open situation, and neither party is at the stage yet where they're ready to stop fighting," one U.S. official said yesterday. "We can't predict the duration with precision, but we think they will be ready in a reasonable time to respond to a mediation effort. So it's very important to get a mechanism ready that will fill that need."

Closely related to the drive for a cease-fire and mediation is the concern, articulated by President Carter on Wednesday, that continued Fighting might choke off freedom of navigation in the Persian Gulf, through which roughly 60 percent of the world's oil is transported.

So far, U.S. officials have been encouraged by the fact that Iran, while declaring its territorial waters in the gulf a "war zone," has not interfered with shipping going to and from other oil-exporting countries of the area.

If Iran continues that restraint and if the fighting is halted within a relatively short time, U.S. officials say, the danger of widespread disruptions in oil supplies will be averted.

If the situation changes and navigation in the gulf is imperiled, the officials say it then would become essential for the United States and its allies to find some means of safeguarding ships in the area.

Several possible methods have been suggested, ranging from formation of a multinational naval force to police the gulf to providing governmental guarantees for shipowners afraid to send vessels into the area because of prohibitive, war-situation insurance rates.

However, the officials stressed, these various options are still in a very early stage of discussion by Washington and its allies; and, at this point, the countries concerned are hopeful that the fighting can be halted quickly enough to render the problem moot.

Another key factor in the situation, the officials noted, is the attitude of the Soviet Union. Although Moscow is Iraq's chief arms supplier and has been trying to score propaganda points by blaming the conflict on the United States, administration sources are encouraged that the Soviets so far seem to be keeping themselves strictly aloof from the fighting.

The Soviet Union is not in as tight a spot as the United States in the conflict. Moscow doesn't gets its oil from the Persian Gulf and could more openly back Iraq without losing too much elsewhere because of Iran's largely isolated position in the world.

Yet, officials believe the Soviets have ample reason to remain neutral since influence in Iran may also be important to them, and any over Soviet involvement, on the heels of Afghanistan and troubles in Poland, could hurt Moscow throughout the Moslem world and among uneasy allies in eastern Europe.

Sources here feel the next four or five days will be crucial on the battlefield.In this assessment, Iraq is more well prepared to carry on a lingering, low-intensity war than is Iran.

Informants say there is no hard evidence that Moscow has rejected supply of spare parts to Iraq. While no major Soviet resupply seems underway, some spare parts are being supplied, sources say.

Iranian forces, equipped mostly with U.S. weapons, are in much worse shape, with serious problems of supply and communication involving command and control over their forces. Through more Iranian planes are flying than some officials thought likely, sources say bombing has been ineffective, presumably because the sophisticated electronic systems haven't been well maintained.

Some analysts believe that the reported haphazard Iranian bombing -- which reportedly has caused more civilian casualties in Iraq than Iraqi raids into Iran -- may be feeding Iraqi anger and intention to keep the battle going.