A bill to overhaul the operations of the United States Patent and Trademark Office is speeding toward a conclusion, but one significant speed bump remains.

Senator Tom Coburn, Republican of Oklahoma, is planning to offer an amendment on how the Patent Office uses the fees it collects. If the amendment passes, which even Mr. Coburn’s staff admits is less than certain, the House and the Senate will have to reconcile competing version of the bill.

The Senate previously voted 95-to-5 to approve Senate Bill 23, which included Mr. Coburn’s language that would allow the patent office to keep all the money it raises from fees for its own operations. The House, however, passed a different bill, HR 1249, which would put excess funds – those above the patent office’s annual budget – into a sort of lockbox that could be used only with Congressional approval. Now, the Senate is taking up the House bill.

The bill would also change the patent system to a “first to file” priority system from its current “first to invent” system and overhaul ways that interested parties can challenge patents.

Currently, all of the excess revenues from patent fees go into the general fund and are used for projects far removed from patents. Leaders in both parties have supported passing a patent bill, and many of them have said the fee diversion is a major contributor to the three-year backlog in patent applications and to the decrepit state of the patent system’s computer networks.

Mr. Coburn’s prediction is that members of Congress will find some way to pilfer the patent-fee lockbox, despite their vows not to. “He thinks it will be a lock box with a hidden door,” said John Hart, a spokesman for Mr. Coburn.

So while a majority of senators might in theory support Mr. Coburn’s change, there is also a strong feeling that it would be better to get the bill finished and onto President Obama’s desk. The alternative – a continuing fight with House Appropriations Committee members and perhaps a conference committee to resolve the differences – would keep the patent issue on Congress’s plate for several more weeks.

With Mr. Obama already regularly highlighting the patent bill as something that Congress can do “right now” to help create jobs, few in Congress see the need to spend more time on the matter.

Democrats are likely to bring the patent bill to the floor for debate on Wednesday. Mr. Hart said that Mr. Coburn realized “it’s an uphill battle at this stage” because “there is a desire to get the bill done.”

If enough Senate Republicans do not back an effort to change the funding language, it is unlikely that a majority of Democrats would go against their leadership’s desire to pass the bill and move on. So brief though it may be, the debate on the Coburn amendment could be a heated one.

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