A small business group is concerned that some employers may not have easy access to an employment verification system mandates in the Senate immigration plan. (David McNew/GETTY IMAGES)

The nation’s largest small-business lobbying group has suddenly inserted itself into the immigration reform debate, raising several concerns about legislation that is nearing approval in the Senate.

Quiet on the issue to this point, the National Federation of Independent Business has sent a letter to Senate leaders, urging them to address several “red flags” for small business owners in the chamber’s nearly finalized immigration package. The group took particular issue with the creation of a new Bureau of Immigration and Labor Market Research, which would measure worker shortages and adjust caps on employment-based visas.

Susan Eckerly, the organization’s senior vice president of public policy, noted that the department would be self-funded using fees collected from businesses that hire low-skilled foreign workers — fees that could increase without approval from lawmakers.

“This self-funding mechanism shields the new Bureau from Congressional oversight,” Eckerly wrote in the letter to Senate Majority Leader Harry Reid (D-Nev.) and Minority Leader Mitch McConnell (R-Ky.). “This structure creates a strong incentive to increase the fees and impose additional and new fees on employers.”

On Monday, the immigration bill cleared an important hurdle as senators voted to move forward on a border-security amendment meant to garner additional support from Republicans. The bill appears to have more than enough votes to pass the Senate, though its supporters are still working to gather as many votes as possible in order to force action in the House.

Republicans have been leery of several components of the legislation, including new rules and regulations for businesses — some of which were highlighted by the NFIB.

For instance, the group has supported legislation that would require businesses to use the federal government’s E-Verify program. Currently voluntary, the online program allows employers to check the work eligibility of job candidates, and it would become mandatory for all firms under the Senate immigration plan.

However, as NFIB points out, the proposed rules do not take into account company size in the program’s fee structure, do not limit the fines for small businesses, and do not address who would pay for new, mandatory E-verify training. In addition, the group asked lawmakers to provide a phone-in alternative to the current E-Verify Website, which would help small firms in rural areas, where Internet connections are harder to come by.

“The tools and technology mandated for E-Verify under S.744 must be affordable, reasonable, and usable for all small businesses,” Eckerly wrote, warning that the current versions of the bill “places significant new costs, bureaucracy, and regulations on small employers.”

Despite its concerns with some of the provisions, NFIB expressed support for broad changes to the current immigration system — as have other small business groups.

The Small Business Majority released a poll earlier this year showing that a majority of business owners support the immigration reform efforts on the Hill, with 64 percent backing proposals to allow more low-skilled workers into the country and 74 percent supporting proposals to help highly trained immigrants.

President Obama on Monday reiterated his support for the bill and its potential benefits for the business community.

“If we get this done — when we get this done — I think every business leader here feels confident that they’ll be in a stronger position to continue to innovate, to continue to invest, to continue to create jobs, and ensure that this continues to be the land of opportunity for generations to come,” Obama said.

Follow On Small Business and J.D. Harrison .