A pattern of murders with apparent official complicity has developed during the past decade in two states of southeastern Mexico with large Indian populations, Amnesty International reported yesterday.

The London-based human rights group said in a report that most of the killings, along with dozens of unsolved disappearances, are linked to longstanding conflicts over land. It said a significant number of victims were members of peasant organizations that oppose Mexico's ruling party.

The report also charged that torture of prisoners is in "common use" in the two southeastern states -- Oaxaca and Chiapas -- as well as other parts of the country.

A response by the Mexican government, published with the report, acknowledged that there had been "regrettable lapses in the administration of justice" but said that when complaints of abuses are presented to the authorities through the correct channels, the perpetrators of the abuses are prosecuted.

The government's response also criticized Amnesty and other human rights groups for publishing the results of investigations that had not been carried out under rigorously high standards. It said such groups often present "long, indiscriminate lists" of names of people who allegedly have disappeared "without any precise facts or basic information about the person, or the place and time of the supposed disappearance."

Amnesty International praised the Mexican government for its cooperation with delegations that visited southeastern Mexico in March 1984 and January 1985. But it disputed a government contention that most cases of abuse that were reported had been investigated and the suspects had been prosecuted.

The report cited the cases of 17 killings in the San Juan Copala area of Oaxaca State. In at least 11 cases, the report said, the victims were members of an antigovernment peasant group. Only two of these cases were investigated and only four persons were arrested. Of these, three were released on appeal.

In three of the 17 cases, in which the victims were supporters of the government's Institutional Revolutionary Party, there were "numerous arrests," almost all of them members of the antigovernment peasants' group, the report said.

Amnesty said that in many cases prisoners being held for trial were blindfolded, beaten, subjected to electric shocks and made to stand up for long periods in efforts to force them to confess. It cited governmental moves to change the laws and Mexico's cooperation with international efforts to end torture. But the report added: "The eradication of torture depends not only on the formal existence of legal guarantees but also on the will of the government to ensure that they are observed in practice."

Special correspondent William A. Orme Jr. added from Mexico City:

The removal of thousands of peasants from hydroelectric dam reservoir sites in Oaxaca and Chiapas has left a legacy of bitter land conflicts. Displaced farmers contend that they failed to receive promised new properties and established communities complain that they have been forced to share scarce farmland with newcomers.

Violent land-title clashes in both states have also been prompted by the rival claims of neighboring villages which, because of rapid population growth, have begun farming previously unused land. In what Mexican authorities say is a disturbing trend, police officers sent in to settle these disputes are increasingly being met by angry residents armed with hunting rifles and shotguns.

On Feb. 12, peasant farmers in the Oaxaca town of Yaxe ambushed some state policemen, killing 17. Some initial reports attributed the massacre to narcotics traffickers, but foreign reporters who interviewed local residents and witnesses to the killing said the battle resulted from a 45-year-old fight over land rights.

Mexico, which often attributes foreign criticism of its internal affairs to the influence of the American "ultra-right," is sensitive to the reports of Amnesty International, which is seen here as a liberal organization. Mexicans have cited its reports in criticizing Guatemala and El Salvador on rights issues.