The Reagan administration has developed plans that include possible military options to be used against Cuba if that country does not permanently halt its flow of arms to leftist insurgents in El Salvador, a senior State Department official said yesterday.

Under questioning from Sen. Christopher J. Dodd (D-Conn.) before the Senate Foreign Relations Committee, Undersecretary of State Walter J. Stoessel Jr. said that in order to halt the arms flow at its "source" the United States has "a wide variety of options under consideration, political, economic, not excluding or necessarily including military."

He said these options involved specific plans and, asked if they also included military plans, replied, "They do not exclude anything."

Stoessel's comments marked the first time that the administration has publicly acknowledged that it has considered military measures in response to the Cuban arms flow to the Salvadoran guerrillas. White House and State Department officials have repeatedly warned that they are prepared to "go to the source" in dealing with the arms flow, but they have been deliberately vague in discussing what this might entail.

Dodd asked for a closed session of the committee to question Stoessel further on the options the administration has developed to deal with the arms flow, but agreed to wait until after Secretary of State Alexander M. Haig Jr. testifies before the committee today.

Haig, who yesterday told a House committee that El Salvador is on a communist "hit list" in Central America, is likely to be questioned closely about the extent of American planning to deal with the arms flow at its Cuban source.

Stoessel's comments came near the end of a long afternoon of testimony during which he and other administration officials defended President Reagan's decision to seek additional military aid for El Salvador and to send 54 military advisers there to aid the government that is headed by President Jose Napoleon Duarte.

Several skeptical Democrats on the committee suggested that the dispatch of the military advisers could be the beginning of another bitter Vietnam experience for the United States. But Stoessel, Gen. Ernest Graves, director of the Defense Security Agency, and other administration officials said there were a number of key differences between the situation in El Salvador and what the United States faced in Vietnam in the 1960s.

"The steps we are taking are very modest," Stoessel said. "The situation is containable."

Democratic opposition to the Reagan administration El Salvador policy was evidenced both by the questioning and by the introduction of legislation sponsored by Sens. Paul Tsongas and Edward M. Kennedy both Massachusetts Democrats, to suspend military aid to the Central American country unless five specific conditions are met. The conditions include a thorough investigation into the killings of four American Catholic missionary women in El Salvador last December and a written request for the military advisers from the Duarte government.

Administration officials said they are satisfied thus far with the extent of Salvadoran efforts to find the killers of the missionaries.

As for the advisers, Stoessel said Duarte, seeking to keep the American presence as small as possible, had personally approved the need for each of the 54 advisers. He said that was considered sufficient U.S. support at present, but he declined to rule out the possibility that there could be a "slight increase" in the number of Americans at some later time.

In another development affecting Latin America yesterday, the State Department praised what it called the progress that has been made on human rights issues in Argentina at the conclusion of the visit to Washington of Argentina's president-designate, Gen. Roberto Viola. The department said the United States hopes to have further talks with Argentine officials this spring concerning "nuclear cooperation," a subject that came up during the Viola visit to Washington.