The budget-cutting fervor that killed earmark spending has sent a panic through the nation’s seaports, where billions of federal dollars have traditionally been directed almost entirely at the discretion of lawmakers.

Anxiety is particularly high because the new route for federal funding, which runs directly through the Army Corps of Engineers, is being forged just as many Eastern Seaboard and Gulf of Mexico ports are eager to expand and capitalize on the widening of the Panama Canal, scheduled to be complete in 2014.

“There is a disconnect with reality in Washington,” said Bill Johnson, the director of the Port of Miami, who has been lobbying furiously for approval of dredging of his harbor in advance of the Panama Canal project. The White House budget did not include the $75 million sought by Miami officials for the project, which Johnson said would generate 30,000 jobs.

In addition, for the budget now being considered by lawmakers to fund the rest of the year, Congress will approve overall spending for the Corps, which then has discretion to parcel out the money as it sees fit. That has significantly lessened local officials’ ability to lobby their federal lawmakers to save their projects and has made them more reliant on executive branch judgments.

Port officials complain their public works projects have been unfairly lumped in with more controversial earmarks that drew public ire, such as a cheese museum or the “Bridge to Nowhere” in Alaska.

“You are not talking about a one-time appropriation for the Teapot Museum in Topeka,” said Byron Miller, a spokesman for the Port of Charleston. The South Carolina port has been seeking funds to study deepening of Charleston Harbor so it can compete for business from the bigger ships. Miller and others say dredging projects boost the economy by drawing more international trade.

The president’s budget for fiscal 2012 did not include money for a $400,000 dredging feasibility study, though it does include a $600,000 grant for the Port of Savannah in neighboring Georgia.

Also exacerbating the problem is that South Carolina’s Congressional delegation has split over how to fund the harbor project.

Sen. Lindsey Graham (R) said he would, as a last resort, try to direct money for the study through an earmark. However, the state’s other GOP Senator, Jim DeMint, an ardent earmark opponent, has argued the solution is for the Army Corps of Engineers to overhaul how it allocates its funds.

Rep. James Clyburn, who has secured millions of dollars in earmarks for the Port of Charleston in the past, said he was unwilling to press the White House for a port study earmark. The Democrat said that it was under pressure from Congressional Republicans that President Barack Obama this year threatened to veto any appropriations bills that included earmarks.

“This is a classic case of be careful of what you pray for,” Clyburn said.

Clyburn, whose district includes the port, said this time he may try to persuade another agency to authorize the study in a way that doesn’t require an earmark.

In Florida, the Miami-Dade Board of County Commissioners, which oversees the port, last week approved a contract for a federal lobbying team, which included for the first time the powerhouse law firm of Patton Boggs. Several commissioners expressed concern, however, that delays in approving the contract may have hampered the port’s ability to secure federal funding for next year.

The Port of Miami’s director said he will keep pressure on Washington. “I may just have to rent an apartment there,” Johnson said.

Advocates of the earmark bans say the Army Corps of Engineers can now make more rational decisions on which ports should be improved. They argue that earmarks resulted in taxpayers footing the bill for unnecessary and expensive public works projects.

Steve Ellis, vice president of Taxpayers for Common Sense, a budget watchdog group, said not every port has to be deepened to accommodate the bigger ships from the Panama Canal. Rather, the lobbying for such projects by local officials amounts to “trying to keep up with the Joneses,” he said.

Now the Army Corps of Engineers will underwrite the most critical projects instead of the ones pushed by politicians with the most clout, Ellis said.

But Kurt Nagle, president of the American Association of Port Authorities, which represents 85 U.S. ports, said lawmakers should have a say in which projects are funded.

“They are closer to the location of these ports and recognize what their benefits are,” Nagle said.

He also noted that even when they were inserted as earmarks, the projects still had to be considered feasible by the Corps.

Nagle said his group was working on convincing lawmakers that these projects should be considered differently from other earmarks. But port officials acknowledged they are unsure of how they will have to go about securing federal dollars in the future.

“We’re all trying to figure out what’s next in how these projects will be funded,” said Miller, the Port of Charleston spokesman.