In a sharp blow to President Reagan's policies in Latin America, the House Foreign Affairs Committee yesterday voted 19 to 16 against the administration's request for $50 million in additional military aid to El Salvador.

Reagan had sought the funds as part of a $110 million emergency infusion to shore up the Salvadoran government against leftist guerrillas. The other $60 million would be shifted from already appropriated funds for Morocco and other countries, but has been held up in a House Appropriations subcommittee.

James Michel, deputy assistant secretary of state for inter-American affairs, urged the committee to approve the $50 million, saying rejection would be "very harmful to our interests in democracy and human rights."

But Rep. Michael D. Barnes (D-Md.), chairman of the subcommittee on Western Hemisphere affairs, said the administration's request would amount to "$50,000 in military aid for every guerrilla we know of."

Six Democrats, including committee Chairman Clement J. Zablocki (D-Wis.), voted for the administration's request. It failed when three Republicans--Reps. Jim Leach (Iowa), Olympia J. Snowe (Maine) and Ed Zschau (Calif.)--voted with the Democratic majority.

The president's request could be revived on the House floor or in the Republican-controlled Senate Foreign Relations Committee. But that committee has already voted to cap military aid to El Salvador in 1983 and 1984 at $50 million a year. The administration has already received $26 million for 1983.

The Senate committee also has indicated that it would like to see negotiations without preconditions between the guerrillas and the Salvadoran government. The administration has adamantly opposed open-ended negotiations, contending they would lead to power-sharing.

However, on the other $60 million the administration is working to meet various conditions laid down by Rep. Clarence D. Long (D-Md.), chairman of the House Appropriations subcommittee on foreign operations, including a suggestion that the administration appoint a high-level envoy to work toward a political solution.

The corresponding Senate Appropriations subcommittee has already approved reprogramming the $60 million, though it too attached some conditions. The Senate Foreign Relations Committee voted to cut the amount.

Yesterday, Zablocki said he would send a letter to Secretary of State George P. Shultz notifying him that the House Foreign Affairs Committee also wants some say over reprogramming requests, which committee members consider to be an end-run around their committee.

To emphasize the point, the committee yesterday cut in half the administration's request for $100 million in additional funds for Morocco, part of which were necessary because Moroccan funds were to be diverted to El Salvador.

Meanwhile, Attorney General William French Smith, who returned Saturday from a 12-day trip to Latin America, said yesterday that he warned the Salvadoran government the administration is not satisfied with its inquiries into the deaths there of eight American citizens.

Smith, whose trip to Mexico, Peru, Bolivia and El Salvador concentrated mainly on drug smuggling problems, said he told Salvadoran officials that the United States wants speedier action in those cases plus long-term improvements in El Salvador's judicial system.

"The bottom line is that this is a matter of substantial urgency," Smith said. "We are supporting that government . . . but it is essential that changes be made in the judicial system and that they be made soon . . . . "