As flags waved and children sang "God Bless America," 56 Soviet Jewish emigres were honored yesterday for becoming American citizens.

About 35 of them registered to vote directly after the ceremony in the Jewish Community Center in Rockville. Almost all said they would vote for President Reagan in the November election.

"He stands strong for this country," said Sofya Khrizman, 34, of Silver Spring. "I only wish he would be younger in a couple of years."

"Mr. Mondale was vice president when we came here in 1979, and that was a time of shame with the hostages in Iran," said Yakov Urevich, 40, of Rockville. "I'm afraid Mr. Mondale is too liberal for us. The communists do not respect you unless you show your strength."

The emigres' strong support for Reagan caused some perplexity for the Americans who had helped them at the Jewish Community Center.

"I think they're just wrong," said Elaine Mann, director of the center's project on Soviet Jews. "But they say we're naive. Anyway, there's a secret ballot here, and what I think has nothing to do with them."

The new U.S. citizens are among about 1,400 Soviet Jews who have settled in the Washington area since the late 1970s. Overall, about 130,000 Soviet Jewish emigres have come to the United States since about 1970 -- a number about equal to those who have moved from the U.S.S.R. to Israel.

The high point of the exodus was 1979 when about 51,000 Soviet Jews settled in the United States. But the number plummeted in 1980, and last year about 1,300 came, according to Rita Simon, a sociologist at American University who has written a major study on Soviet Jewish emigration.

It takes five years of residence in the United States to become an American citizen, and most of those who were honored yesterday said they came here in 1978 and 1979.

"It's not always easy to begin a new life," Bella Dantsker of Hyattsville told the audience of about 300 persons in the center's auditorium. "We left because we couldn't stand the Soviet totalitarianism and anti-Semitism anymore. We appreciate the privilege of being American, being Jewish and being free."

Dantsker, who taught Russian language and literature in Kiev, teaches Russian at the Foreign Service Institute. Her husband, Eduard, who taught high school and college chemistry in Russia, works as a chemist for a consulting firm in Rockville. But he said that before he could speak English well he had to take jobs as a darkroom technician. "There is opportunity here," Eduard Dantsker said. "You have to work hard, but you are free."

U.S. District Court Chief Judge Frank A. Kaufman of Baltimore and Montgomery County Circuit Court Judge Stanley B. Frosh took part in the ceremony.

When it was originally planned the ceremony was supposed to include the actual swearing in of the new citizens. But last week Kaufman notified the organizers that he would not allow the actual ceremony to be moved out of the courthouse and into the Jewish Community Center because of "constitutional considerations" about the separation of church and state.

Yesterday Kaufman greeted the new citizens warmly, but he said he wanted them to be treated "like all other new Americans and not part of a separate group."

Of the 40 adults who are becoming citizens, 30 were sworn in in Baltimore federal court on Friday, eight were administered the oath by Frosh at a private ceremony early yesterday afternoon, and two will be sworn in in Baltimore this month.