MANILA, Philippines (AP) _ Army troops battled about 40 Communist rebels for two hours today in the first reported fighting since the end of a cease-fire.

A police source said 18 people were killed, 12 of them civilians caught in the crossfire.

The report said three civilians were wounded in the gunbattle, which erupted at dawn on the outskirts of Lupao, about 90 miles north of Manila.

Earlier reports put the casualties at 12 dead, including an army lieutenant and 11 rebels. But a police source, speaking on condition of anonymity, said a later military report showed the lieutenant, five rebels and 12 civilians were killed.

Brig. Gen. Eugenio Ocampo, military commander for central Luzon, dispatched army and constabulary soldiers backed by helicopters to pursue the rebels, who fled into the hills.

It was the first reported clash with the rebel New People's Army since a 60-day cease-fire expired Sunday. The government's chief negotiator said he doubted peace talks could be resumed on a national level.

Military and media reports say about 30 people have been killed in scattered clashes since the two sides suspended peace talks Jan. 22. The rebels later formally withdrew from the peace effort.

Teofisto Guingona, the government's peace negotiatior, said he met Sunday with an emissary of the National Democratic Front, a Communist-dominated umbrella group that had negotiated on behalf of the rebels. Guingona said he urged the emissary to ask the guerrillas to drop their opposition to the Philippines' new constitution as a basis for negotiations.

''Their premise is that the constitution is anti-people, imperialistic and elitist,'' Guingona said. ''This is not so.''

The constitution was approved by 76 percent of the voters in a national plebiscite Feb. 2.

Among other things, the constitution confirms Mrs. Aquino's term in office until 1992 and makes no provision for the coalition government sought by the rebels.

Asked if he was optimistic the rebels would return to the negotiating table, Guingona replied: ''No, except it is our understanding that there is a segment or part of their structure which is of the belief that it is best for the revolutionary movement to change to the parliamentary process today.''

Guingona said Mrs. Aquino's government finalizing ''mechanics'' for beginning peace talks with regional rebel leaders in six areas.

He did not identify the areas. During the cease-fire, rebel groups in several regions expressed interest in continuing local talks even if the national truce broke down.

But several regional commanders, including those in northern Mindanao, the Visayas islands and parts of Luzon, withdrew the offer and returned to the hills when the national talks broke down last month.

Guingona said that over the next five months, Mrs. Aquino would issue a series of executive orders on social legislation, apparently with the aim of undercutting rebel claims that the government is dragging its feet on reform.

Mrs. Aquino meanwhile met with 18 military officers to discuss problems in the armed forces. Many officers have criticized her as too soft on the rebels and some took part in a failed uprising Jan. 27.

Among those attending was Col. Gregorio Honasan, who has been linked to another failed coup attempt last November.

Presidential spokesman Teodoro Benigno said Mrs. Aquino listened to the officers' complaints about pay and ''assured them they were part of the government.''

She also told them she does not blame the entire armed forces for the 1983 assassination of her husband Benigno, who was murdered while in military custody.

''Despite the death of Ninoy (Benigno), I am not prepared to blame the Armed Forces of the Philippines for some actions of misguided elements,'' she told the eight colonels, four majors and six lieutenants.

The officers pledged their loyalty to the president, Benigno said.

He said Mrs. Aquino will continue to ''touch base'' with other officers, possibly as a monthly fixture. ''She even gave them her telephone number,'' said the spokesman.

Meanwhile, the government's Philippine News Agency reported that 39 constabulary troops who took part in last month's coup attempt in Manila have been dishonorably discharged. The agency quoted the regional commander as saying the 39 would be charged with rebellion before civil courts.