D.C. school board member John E. Warren, chairman of the committee that oversees the school system's finances, was said by school officials yesterday to have collected twice on more than $600 worth of expenses be incurred at a national education conference in San Francisco last month.

According to records in the D.C. public school finance department, the school system issued Warren a $404 airline ticket and $280 in an expense advance to attend the annual conference of the National School Boards Association. Warren yesterday submitted an expense voucher for an additional $36.

In addition, a spokesman for the National School Boards Association said Warren was issued a check on May 6 for $591.50 to cover the same expenses. Warren is a member of the association's board of directors.

The association spokesman said Warren was issued this check after he submitted a voucher on April 28 for his expenses during the San Francisco trip.

Warren said yesterday "I am not in receipt of any double payment." When asked about the two sets of expense vouchers -- one to the national association, the other to the school board -- he said he had been issued a check by the national association, but that he, in turn, has sent them back a check in the same amount. The NSBA spokesman said the check was received late yesterday.

Warren said he "had the option" of billing either the public schools or the national association for his trip and chose to bill the school system, which is facing its severest financial crucnh ever, because he felt the national conference for school board members is a "legitimate expense."

Warren, whose wife accompanied him on the trip, said he was "obligated" to also submit expense vouchers to the national association. Warren said he paid his wife's expenses.

Board President R. Calvin Lockridge said he intends to recommend that the matter be referred to the D.C. inspector general and D.C. board of Elections and Ethics.

According to school sources, Warren tried yesterday to pull back his expense account once it had been submitted to the system's finance department. Sources said, however, said the department's director, James Boyle, refused to give it back.

Warren later denied that he tried to retrieve the voucher.

Allegations about Warren's expenses came to light yesterday as his finance committee was meeting to make crucial decisions about what programs to cut back on in the 1981 school year. The system is facing a $26 million budget deficit for the upcoming school year and Superintendent Vincent E. Reed has proposed eliminating 700 teaching positions and cutting back on preschool and adult education programs.

Warren, who has been critical frequently of wasteful spending in the schools, stayed for six days in a $98-a-day room at the San Francisco Hilton, according to his expense account.

Lockridge also reported yesterday that board member Frank Shaffer-Corona was issued a round-trip ticket for official school business from Washington to Dallas in addition to a ticket from Washington to San Francisco for that conference.

But instead of going to Dallas, to meet with members of a Hispanic nonprofit educational organization, Shaffer-Corona said he combined the two tickets and actually went of a trip that took him from Washington to San Francisco, Mexico City, Dallas and then back to Washington.

Shaffer-Corona acknowledged that the route evolved from his $363 ticket from Washington to Dallas and his $404 ticket for San Francisco. He said he went to Mexico to talk about cultural exchange programs between Mexicans and Americans and to meet with a Palestinian Liberation Organization representative there.

Lockridge said he felt that Shaffer-Corona has taken school funds for one purpose -- to go to Dallas to speak with representatives of the Hispanic organization, Project SER -- and then used those funds for another purpose. He added that he would recommend to the board that the matter be referred to the elections board and inspector general for investigation.

Shaffer-Corona contended that the trips were legitimate and that the project SER people were supposed to meet with him at the Dallas airport but failed to do so.

Lockridge said that Shafer-Corona also violated a board rule that prohibits members from using school funds for international travel. This rule was aimed specifically at Shaffer-Corona who has traveled to Mexico and Cuba in the past at the school system's expense.

After the ruel-making, Shaffer-Corona, who spent a month in Beirut earlier this year was said to be responsible for $2,000 worth of phone calls made between Washington and Beirut and charged to the school board. Lockridge said. Shaffer-Corona was in Beirut on an aborted mission to get into Tehran and help negotiate the release of Hispanic hostages in the American embassy.

School board member Carol Schwartz said the board is still trying to collect on the phone calls Shaffer-Corona put through to the militant students holding the American hostages in Tehran.