A federal judge in Alexandria said yesterday he would permit Virginia real estate magnates Peter and Paul Pomponios to serve staggered prison terms for their tax fraud convictions so that one of the brothers could conduct family business while the other is in prision.

Judge Oren R. Lewis ordered Paul Pomponio to begin serving his three-year sentence on Saturday.

He was sentenced three years ago to serve three concurrent three-year sentences and fined $15,000. His brother Peter was convicted of similar charges and received the same sentence.

Lewis' order directed Peter Pomponio to begin serving his sentence the same day as the release of Paul Pomponio or his older brother Louis Pomponio Jr., whichever is freed first. Louis Pomponio is in jail on other fraud charges and is eligible for parole in May.

Peter and Paul Pomponio have asked U.S. Circuit Court of Appeals Judge Emory Widener to have them released on bond until they can ask the U.S. Supreme Court to review their case. Lewis refused yesterday to grant them release on bond. The Pomponios' attorney then asked that their sentences be staggered so they would be able to conduct their business.

The three Pomponio brothers had a multimillion-dollar real estate empire when their financial and tax problems came under investigation in 1972. Since then, as their creditors seized some of their vast holdings and the empire shrank, the Pomponios have had to defend themselves in a series of civil and criminal proceedings in federal courts.