A peppery opposition mayor in Mindanao was shot dead today. President Ferdinand Marcos denounced the killing and ordered the acting armed forces chief to investigate.

The assassination of Mayor Cesar Climaco of Zamboanga City was the first of a nationally known opposition figure since the death of ex-senator Benigno Aquino Jr. in August 1983.

Climaco, 68, who often walked or rode his motorcycle unescorted around the city 500 miles south of Manila, was shot in the head while inspecting damage at a nightclub that burned last night, initial reports said. A news agency said four suspects were later arrested.

Elected to a third term in 1981, Climaco won a seat in the National Assembly last May but did not assume the office, saying he preferred to remain as mayor.

Climaco was a leader of the opposition Unido grouping. Its president, Salvador Laurel, said, "There seems to an emerging pattern to eliminate or reduce the number of opposition members either by bullet or by the Commission on Elections." He referred to the recent ouster from the assembly of opposition member Aquilino Pimentel because of an alleged election fraud.

In the past three months, a regional opposition leader and three journalists who had written on social-justice issues were slain in Mindanao.

Lt. Gen. Fidel Ramos, the acting chief of staff ordered by Marcos to conduct an investigation into Climaco's death, said he will fly to Zamboanga City Thursday.

Climaco was fond of sending telegrams to Marcos accusing him of election frauds, although the two appeared to be convivial antagonists. In 1978, protesting domination of politics by Marcos' party, Climaco fielded what he called a "crackpot slate" whose candidates included a village clown.

Climaco wore his white hair long, having vowed not to cut it when Marcos declared martial law in 1972. His swaggering style seemed to fit into the cowboy image of Zamboanga City, where bandits seem numerous and Moslem rebels in the hinterland have fought a secessionist war for 12 years.

The bogged-down prosecution of the Aquino case took another turn, meanwhile, with one of the lawyers who conducted the original investigation charging the government prosecutor with incompetence.

In a letter to Marcos -- who had directed the board to assist the nation's ombudsman in laying down the charges -- the board's general counsel, Andres Narvasa, said it was the duty of the prosecutor.