The letter by Ambassador of El Salvador Miguel A. Salaverria {''Why El Salvador Deserves Military Aid,'' Sept. 5} defends the Jesuit murder case as the ''most extensive and efficient criminal investigation in the annals of El Salvador.'' But that's not saying much. These ''annals'' show that over the past decade Salvadoran security forces have killed thousands of noncombatants, but not one soldier has been brought to justice for war crimes.

The ambassador states that ''nine military officers and soldiers have been arrested, including a colonel.'' But it's too soon to praise the investigation. Not one soldier has voluntarily come forward with information in the case, crucial military logbooks have been burned and there is still no official record on the ''confessions'' of those arrested. There are also questions about how Capt. Herrera came to know about the murder of the Jesuits before the news was broadcast on commercial radio.

The ambassador joins The Post editorial {''An Eye On El Salvador,'' Aug. 22} in calling the FMLN negotiating position ''outlandish.'' The proposal of the FMLN for a comprehensive reform of the armed forces was not a condition for further negotiation; in fact, it was agreed that negotiations continue this month. The FMLN proposal offers a good tool for invoking a counter-proposal for military reform. The armed forces cannot reform themselves because corruption and criminal activity are institutional, not incidental.

The ambassador is also concerned that ''individual criminal acts by extra-legal groups should not determine U.S. foreign policy toward our government.'' But it was not an extra-legal group that murdered the Jesuits, their housekeeper and her daughter. It was a criminal act by a legal group: the Salvadoran army. In any case, that a group is ''extra-legal'' does not make it bad. Revolutionaries are always extra-legal. The human rights measure must be brought to bear against both legal and extra-legal groups in civil war. It appears that the ambassador reflects his government's worry that Congress and the American people have had enough with funding systematic crimes committed by ''legal'' groups in El Salvador. FREDERICK B. MILLS Hyattsville