Even as it appeared Sen. Arlen Specter (R-Pa.) had overcome conservative pressure to prevent him from becoming the next Judiciary chairman, Republicans approved a new rule that GOP centrists charge is intended to suppress dissenting voices in the Conference.

By a one-vote margin, Republican Senators agreed to grant Majority Leader Bill Frist (R-Tenn.) the ability to make appointments to influential committees — a power centrists fear will be used to punish them by denying a Senator a seat on a desirable panel if that person opposes the leadership on policy matters.

“There is only one reason for that change and it is to punish people,” griped Sen. Olympia Snowe (R-Maine), who has been outspoken in her opposition to efforts to rewrite the GOP’s rules.

Tradition had dictated that seniority was the sole determining factor in a Republican Senator’s climb up the committee ladder, which can eventually lead to a chairmanship, larger staff, control over sizable budgets and considerable influence in crafting legislation.

Frist and future Republican leaders will now have direct input into who will gain seats on panels such as Appropriations, Armed Services, Finance and Foreign Relations. The new rule allows the Republican leader to name at least half the members of “A” committees.

“It is an opportunity for the leader to have the ability to pull people forward who may not be in line for seniority, to have the opportunity to serve on a committee that they [would] not otherwise because they can either add to the Conference — and the Conference needs,” said Senate Republican Conference Chairman Rick Santorum (Pa.).

Santorum made reference to the fact that Democratic leaders can reward their colleagues by giving them plum assignments for agreeing to shoulder more responsibility. Just this week, incoming Minority Leader Harry Reid (D-Nev.) announced that Sen. Charles Schumer (D-N.Y.) would join Finance in the 109th Congress, after he agreed to serve as the next chairman of the Democratic Senatorial Campaign Committee.

“It could be, as we see with Senator Schumer, an incentive to give him a Finance slot in order for him to take the DSCC chairman,” Santorum said. “Those are the kinds of things that the [GOP] leader has no flexibility to do.”

Sen. John McCain (R-Ariz.), who is known to buck his party leadership, described the rules change in one word: “Bad.” McCain was not the only Republican who had reservations about rewriting the rule. It passed by one vote, 27-26, on a secret ballot. It is unclear which two Senators did not vote.

Rules and Administration Chairman Trent Lott (R-Miss.), who helped draft the rules change, said they were able to win by cobbling together a diverse group of Senators from every corner of the Conference.

“It was not pure,” said Lott, describing a vote that did not fall along the lines of traditional alliances. “It wasn’t purely Old Bulls and moderates against everybody else.”

The rule will not hurt Snowe personally, because it does not allow the Republican leader to reassign Senators to other committees. But the Maine Republican said it presents the image that the GOP is not a party of inclusion.

“It is not a sign of strength, it is a sign of weakness,” she said. “It is a punitive instrument to suppress diverse views.”

At least one moderate, though, shrugged off the rules change. Sen. Lincoln Chafee (R-R.I), who until recently toyed with the idea of leaving the Republican Party, said it was “not going to affect” his decision to remain and noted that Frist and Majority Whip Mitch McConnell (R-Ky.) both contacted him to tell him they would help him get re-elected in 2006.

“That makes a big difference,” Chafee said. “I have big differences with the president, but I also have an election in 2006 and sometimes those things come in conflict. But I have got to look out for my state and I am in the majority and that is important.”

During their organizational meeting, Republicans also agreed to allow GOP Senators to retain only one “B” committee assignment in the 109th Congress. A proposal that would have allowed current members of the Intelligence Committee to remain on the panel was never presented for a vote.

The rules changes were the result of recommendations made by a task force of Republican Senators who began meeting in June to review the Conference’s rules.

“I think only time will tell,” said Sen. Larry Craig (R-Idaho), a supporter of the changes, on the effect the changes will have on the Conference. “I think the leadership will use it very judicially for the positive effect of the Conference.”