I am all against taking bribes and storing the cash in the freezer, but I am also with the Speaker and the many members of Congress who were outraged that FBI agents raided a congressional office last Saturday night.

In this country, we have a separation of powers, which means that the executive branch shouldn’t be poking around legislative offices without consent from Congress.

We need a strong Public Integrity Section in the executive branch. It is not a replacement for the long-overdue strengthening of the congressional ethics committees; both are needed. And the section uses tough measures. It makes some squirm to see video of members of Congress on the take, or members wired to finger lobbyists or their fellow members. But this is what it takes to root out bribery, which is by its nature a crime committed secretly between a public official and an outsider.

It is sad but true that we need corruption probes more than ever. It has become a parlor game in Washington to estimate how many members will be indicted in the 109th. William Jefferson (D-La.) seems like he’ll be next. Duke Cunningham (R-Calif.) is already sitting in prison in what at first seemed like an isolated bribery case but now threatens to encompass a number of members involved in defense appropriations. There are allegations about West Virginia Democrat Allan Mollohan’s cozy relationship with contributors. And, of course, there is the Abramoff scandal, which many believe will produce the most indictments of all.

In this climate, we should applaud the tenacity of the Justice Department’s Public Integrity Section … up to a point.

But the raid of Jefferson’s congressional office goes too far. Not because there was no reason to look there, not because the FBI should never set foot on Capitol Hill, but because the Congress is owed deference as an independent branch of government in clashes with the executive.

Reverse the roles and imagine a congressional committee frustrated that it has not received the documents it is looking for from the president. How would the president react if the sergeant at arms, backed by the Capitol Police, showed up at the West Wing with an hour’s notice and carefully sorted through White House documents to find what it needed?

The constitutional protections for Congress are both specific and general. Specific language protects members against arrest for most charges while attending or going to or from a session of Congress. More important, the Speech and Debate Clause prevents punishment in the legal system for anything done in the course of a member’s official duties. The Framers had in the back of their minds the abuse of Parliament by kings. And courts have used the Speech and Debate Clause to defend members’ ability to read leaked information into the record, as in the Pentagon Papers case, but have limited it in quirky ways, such as allowing the internal publication but forbidding the public distribution of certain information.

But more than these specific protections for members, Congress as an institution deserves respect. The personal office of an individual member is ultimately under the control of Congress as an institution. Congress has a responsibility to protect its members, their documents and its official business. The fact that the Speaker of the House was not fully informed about the raid and there was no haggling between the branches makes this case especially egregious.

Interbranch conflicts are messy. Some matters of importance are not addressed or are delayed because of these conflicts, but the greater good of the independence of our institutions is served.

Fortier is a research fellow at the American Enterprise Institute.