Honduran fighter planes and a Nicaraguan patrol boat clashed in the Caribbean yesterday, officials of both nations reported, in the third naval incident involving Nicaragua and its neighbors in a week.

The two previous clashes occurred on the Pacific Ocean side of the Central American isthmus, in the Gulf of Fonseca, which the United States says Nicaragua is using to smuggle weapons to antigovernment insurgents in El Salvador. Nicaragua's Sandinista revolutionary government denies supplying the Salvadoran guerrillas and accuses the United States and Honduras of backing "counterrevolutionaries" operating in the area of yesterday's incident.

The reports of the new clash came as Mexican Foreign Minister Jorge Castaneda arrived in Nicaragua on a diplomatic campaign to ease growing tension throughout Central America. Reuter reported that Castaneda spent the weekend in Havana briefing Cuban officials on his talks March 14 with Secretary of State Alexander M. Haig Jr.

The United States has authorized Mexico to hold exploratory talks on Mexican peace proposals for the region with Cuba and Nicaragua, the countries the Reagan administration has accused of providing weapons to Salvadoran rebels. The Mexican proposals involve efforts to improve relations between those two countries and the United States, then move for a negotiated settlement to the fighting in El Salvador.

According to a statement by Nicaraguan Foreign Minister Miguel D'Escoto, yesterday's clash began when a Nicaraguan Coast Guard ship seized two Honduran "pirate" boats that had entered Nicaraguan waters "to engage in illegal activities." D'Escoto said the Nicaraguan patrol ship, the Tayacan, was attacked by Super Mysteres of the Honduran Air Force, and fired back, hitting one of the Honduran planes.

The Honduran Foreign Ministry said an unspecified number of Nicaraguan patrol boats seized four Honduran fishing boats in Honduran waters. It said the Nicaraguans fired first and one Honduran plane was hit.

"This logically prompted the Honduran planes to fire on the boat that had opened fire," the Honduran statement said.

Nicaragua reported last week that on Monday a Honduran patrol boat machine-gunned a Nicaraguan fishing boat in Nicaraguan waters in the Gulf of Fonseca. Two employes of the nationalized fishing company were reported missing. Two days later, the Nicaraguan Foreign Ministry said, a Salvadoran patrol boat fired on a Nicaraguan vessel, wounding one man.

The Pentagon disclosed in February that U.S. destroyers with sophisticated monitoring equipment have been stationed in the Gulf of Fonseca since late last year.

The incidents at sea have added to the growing tension in the region as the civil war in El Salvador spreads beyond its borders. The government of Nicaragua has stepped up its charges that the United States and neighboring Central American countries encouraged recent raids and sabotage attempts by anti-Sandinista rebels, most of them based in Honduras near the northeastern region of Nicaragua.

Managua's concern grew after The Washington Post reported March 10 that President Reagan had authorized covert action to weaken the Sandinista government and the building of a paramilitary force to block the alleged Cuban-Nicaraguan arms supply network in Nicaragua and elsewhere.

Nicaragua declared a state of emergency March 15 and on Friday asked the U.N. Security Council to consider Nicaragua's accusation that an invasion by U.S.-backed rebels is "imminent."

Honduras said yesterday that it would ask the Organization of American States to hold a meeting on the alleged border violations by Nicaragua, The Associated Press reported from Tegucigalpa.

The State Department yesterday criticized the deportation of "18 to 20" Jehovah's Witness missionaries, 10 of them U.S. citizens, from Nicaragua over the weekend.

Spokesman Dean Fischer said the Nicaraguan action "represents a flagrant violation of freedom of expression and is, regrettably, only the latest in a series of acts by the Sandinista government to deny basic freedoms."

He said the United States deplores "these repressive acts which raise serious questions about the Nicaraguan government's interest in maintaining a pluralistic society or improved relationships with its neighbors and the United States."

News services reported that Nicaragua's Interior Ministry said the missionaries were told to leave because they published propaganda defaming the military and discouraged Nicaraguans from joining a civil defense program that was stepped up in the state of emergency.

Illustrating the level of tension in Nicaragua, the government issued a statement yesterday urging all private and state-owned industries to "work at full steam" to guarantee supplies in case of war with U.S.-backed forces.

Vice Minister of Industry Gilberto Guzman said the government has "everything ready" to put the country on a wartime footing.