A three-judged federal panel in Washington yesterday turned down challenges brought by the Federal Election Commission and Common Cause against political committees that have pledged to raise millions of dollars for Ronald Reagan's presidential campaign.

President Carter's campaign counsel, Timothy G. Smith, said last night that the Carter reelection committee will continue to attack, both in the FEC and in the courts, the legality of the independent committees. In the meantime, Smith said,"we remain at a very serious disadvantage . . . ."

The judges issued two separate orders yesterday, without written opinions, saying an "expedited" decision was required because of the "nature of the case saying an "expedited" decision was required because of the "nature of the case." Written explanation will follow, they said.

The three-judge court denied the FEC's request that it uphold the constitutionality of a portion of public finance law which says the unauthorized political committees cannot make expenditures over $1,000 on behalf of candidates who accept public financing. Attorneys for the committees were independent of the candidate.

In 1976, the U.S. Supreme Court athrew out the part of the Federal Election Campaign Act that limited expenditures by individuals and groups. The independent committees have interpreted this ruling as exempting them from a separate, $1,000 expenditure limit in the Internal Revenue Code. The FEC wanted the three-judge panel to declare that provision constitutional and applicable to the independent committees.

The court, without explanation, denied the FEC's request and ruled in favor of the committees. One lawyer familiar with the cases said yesterday that it was unclear from the brief orders whether the judges had found the law unconstitutional or had simply decided that it was inapplicable to the case.

The issues were heard by the U.S. Appeals Court judges Edward A. Tamm and Malcolm R. Wilkey and U.S. District Court Judge John Garrett Penn.

Fred Wertheimer, a senior vice president of Common Cause, said late yesterday that the lobbying organization will take the case to the Supreme Court. "We intend to pursue this matter in every way we can," Wertheimer said.

A spokesman for the FEC said late yesterday that it would not comment until it received the court's full opinoion.

Common Cause, which had joined with the FEC on the constitutionality issue, further contended that the committees were not truly independent because their activities and officials were closely interwined with the Reagan campaign.

In the Common Cause case, which was brought separately from the FEC action, the three-judge panel dismissed the question about the committee's independence, saying the court did not have jurisdiction over that. The committees had contended that any challenges to their independent status would first have to be brought before the FEC.

The FEC went to the federal court for a ruling on the constitutional question after the Carter campaign and the Democratic National Committee filed a complaint with the agency saying that the Reagan campaign should not get public financing if it was the beneficiary of money raised by independent committees created by prominent Republicans.