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Still, URS has spent well in excess of a half-million dollars lobbying Congress so far this year on energy and water appropriations, among other issues.

Steve Ellis, vice president of Taxpayers for Common Sense, a watchdog group, said the project has been poorly run and beset by delays, and shouldn’t have been included in the stopgap bill.

“It seems to me that it just didn’t rise to that level of importance where it should have been included,” Mr. Ellis said. Lawmakers “could’ve dealt with this another way.”

What appeared to irk lawmakers the most was that the project was added to the bill at the last minute — unlike other special items, such as the $174,000 death gratuity payment to the widow of the late Sen. Frank R. Lautenberg, which, while controversial, had been in previous versions of the bill.

Indeed, the haphazard bill-writing Wednesday led to a scene with Senate aides poring over the language in a backroom off the Senate chamber Wednesday afternoon, when their bosses were going to be asked to vote less than two hours later.

Early drafts of the bill floated around online, including special projects that senators ended up striking.

One of those would have approved building an additional Coast Guard cutter, at a cost of nearly $600 million.

Another section that would have specifically spent $20.6 million on the Office of Special Counsel was dropped later in the process. That office protects federal employees from whistleblower retaliation, political pressure and other prohibited practices.

A Senate aide said the provision was dropped at the insistence of Sen. Mike Johanns, Nebraska Republican. Mr. Johanns’ office didn’t respond to messages left seeking comment Thursday evening.