A U.S. Marine captain loaded his .45-caliber pistol and raised it in ready position to face down three Israeli tanks attempting to charge through a jointly manned U.S.-Lebanese Army checkpoint here today, according to the U.S. commander of the Marine contingent in the multinational force.

When two of the Israeli tanks made a second try, racing toward the checkpoint at battle speed, Col. Thomas M. Stokes Jr. said, the Marine captain jumped on top of the third tank and yelled at the Israeli commander until he gave orders for the other two to stop.

Stokes said that after the confrontation ended, the Israeli commander told the Marine captain, "One thing we don't want to do is shoot each other."

According to Stokes, the captain, Charles Johnson, 30, of Neenah, Wis., replied, "Yes, but you keep doing things like this and that likelihood is going to increase."

The encounter appeared to have been the most serious of several incidents during the last month involving Marines and Israeli soldiers. The two groups have adjoining areas of operation but little direct contact because of U.S. concern that this might leave the appearance that the Americans are operating in coordination with the occupying Israeli Army here.

About two hours after the incident, what appeared to have been a 75-mm tank round exploded about 50 yards from another Marine position along the runway of Beirut International Airport. No one was injured in the blast, Stokes said.

The Marine commander said Israeli officers called on a hot line immediately after the explosion to inform him that their troops had not fired the round. Stokes said he believed them and he speculated that it had probably ricocheted from the hills overlooking Beirut where Christian and Moslem Druze militiamen have been engaging in heavy artillery duels in recent days.

Meanwhile, three gunmen in a speeding car opened fire on a group of French Marines jogging in a Moslem sector of Beirut. One Marine was reported in serious condition with two bullet wounds in the stomach and the other was wounded in one arm.

A meeting last week, bringing together Stokes and special Middle East envoy Morris Draper with Israeli Northern Commander Gen. Amin Drori for the first time, had attempted to resolve differences between their two forces. But they left in disagreement over their boundaries. That lingering dispute over boundaries appeared to be behind the problems here today.

In Washington, the Israeli Embassy issued a statement saying the three tanks had been in territory they were authorized to patrol under an agreement reached at last week's meeting. "We reject the allegations . . . that there was any attempt to cross the American lines, or to challenge the Marines," the statement said.

Stokes and his press spokesman have generally attempted to play down the recent incidents, although they have raised strong expressions of concern at the Pentagon, including statements by Secretary of Defense Caspar W. Weinberger.

Nearly eight hours after today's incident, Stokes--at a previously scheduled press conference--made no mention of it.

The Marine colonel said he had told the Israelis it was "okay to operate" in the areas where the boundaries are disputed "but I have a company sitting there, and don't screw with them."

Later, after the Marines here reported the incident to Washington, Stokes and his aides confirmed the confrontation to reporters here, explaining that they had not done so earlier because the incidents were classified information.

"We've got a classic situation in which we were caught between a rock and a hard place," Marine spokesman Capt. Dale Dye said.

At the press conference, Stokes had spoken confidently about the Marine operation here and had suggested that his troops were ready to have their operation expanded.

"I've got some pretty cocky Marines here who think that no matter where they go, nobody really is going to be shooting at them and the shooting is going to stop," he said. "Now I don't know whether that's true or not. Nobody's ever going to know until we go there."

He indicated that some Marines were restless to go to areas where fighting continues in this war-torn nation. The attitude, he said, was: "Come on colonel, let me get out and go stop this crap."

The 1,200 Marines here have been the least visible of the 4,300 troops in the multinational peace-keeping force sent here in late September. Italian and French soldiers roam freely through much of the city but Marines have generally been confined to their positions around Beirut airport, going on liberty only as part of specially organized tours into the city.

But their responsibilities near the airport have drawn them into incidents with the Israelis, who have charged that the Marines have permitted terrorists to slip behind their lines and attack Israeli convoys.

The efforts by Israeli soldiers to penetrate Marine positions have followed those attacks. In the latest terrorist attack, which occurred Sunday several miles north of the Marine position, one Israeli soldier was killed and four others were wounded.

Stokes, at his press conference today, discounted the Israeli charges.

"Nobody's given me any information, including the Israelis, that the hit-and-run guerrillas are coming out of this village or that village," he said.

In the incident at the checkpoint this morning, Stokes said Capt. Johnson walked along about 200 to 300 yards in front of the checkpoint to stop the tank unit when he saw it approaching the position.

The Israeli commander, Stokes said, insisted that he had the right to move through the area. But, Stokes said, Johnson told him, "The only way you can come is to go over me." At that point, the Israeli commander got in his tank, revved up his engine and said, "I'm coming anyway."

Johnson then unholstered his .45-caliber pistol, loaded a magazine, and raised the weapon at a 45 degree angle in the air. At this point, Stokes said, the tank commander turned off the road and moved slowly away from the checkpoint. But the Israeli commander then gave a signal to other tanks and they made a dash back up the road at battle speed.

It was at this point, Stokes said, that Johnson jumped on the commander's tank and shouted, "You better stop those guys!" Stokes said Johnson did not aim his pistol at the Israelis, but yelled until they stopped.