President Carter decided only Thursday evening, the might of his inauguration, that he would issue his Vietnam-era pardon on his first full day in office, according to a Carter official.

Carter and his advisers, with their quick action, apparently sought to head off any congressional efforts to arouse anti-pardon groups.

Sen. James B. Allen (D-Ala.) had been pushing a resolution opposing any pardon.

The White House received numerous angry telephone calls Friday protesting the pardon, which was condemned by traditional veterans groups.

New Hampshire Gov. Meldrim Thomson yesterday ordered all American and state flags flown at half mast Monday through Friday to protest the pardon. The Republican conservative said Carter's pardon will be remembered by millions of Americans the same way they remember Japan's strike against Pearl Harbor.

As Carter predicted, the pardon also left advocates of total amnesty unhappy, since it included only draft evaders who did not commit violent acts and exluded deserters and men with less than honorable discharges.

David Berg, the Carter transition official who worked on the pardon, said yesterday that he expects the initial opposition to die down and "people will come to see that the President's taken a courageous position politically." Carter promised during his campaign to pardon draft evaders.

Berg said that he and the senior adviser on the pardon question, Carter's close friend, Charles Kirbo, agreed early that deserters and men with bad discharges should not be pardoned.

"The record-keeping is awful," Berg said. "The military records are at best incomplete and confusing." Thus, he said, one cannot determine from reading a discharge record whether the reason given covers a more serious offense as the result of a form of plea bargaining or whether it is invented to cover a political offense related to antiwar activity.

Carter has ordered a study of the problem.

"The more they study it, the more they'll move toward a compassionate decision," Berg predicted.

Berg acknowledged that pro-amnesty groups were probably right when they counseled the pardoned draft evaders not to rush back from exile. It will take a week or 10 days to get instructions to immigration field offices, he predicted.

The Justice Department was trying to determine what definition of "violence" Carter's pardon used, since draft dodgers who committed violent acts are excluded from the pardon.

By far the largest number of beneficiaries of the pardon are men who never registered for the draft. Although they faced only slight chance of prosecution, they now face none. Estimates of their numbers run from 200,000 up to a million.

About 13,000 draft evaders benefit from the pardon. Most of them, about 9,000, had been convicted or pleaded guilty to draft offenses and been punished.

Berg said that seven men would be released from prison because of the pardon.