Disagreements are emerging between Congress and the Federal Communications Commission over how much spectrum should be set aside for unlicensed uses, such as Wi-Fi, as part of upcoming spectrum auctions.

The auction legislation passed by Congress earlier this year as part of the payroll tax cut extension (PL 112-96) nearly stalled over the issue of unlicensed spectrum. This free spectrum is used in technologies such as remote controls and wireless computer mice and could be deployed in the future for citywide wireless Internet access known as Super Wi-Fi.

Ultimately, California Reps. Anna G. Eshoo, a Democrat, and Darrell Issa, a Republican, reached a compromise that instructed the FCC to make space for unlicensed spectrum in “guard bands” — the unused areas around a licensed spectrum block that will be set aside to avoid interference among users.

But now Eshoo is suggesting that congressional deal is under threat as the FCC begins laying its plans for conducting the spectrum auctions. Eshoo wrote directly to FCC Commissioner Ajit Pai, a Republican, taking issue with his characterization of the law at an agency meeting last month where he suggested the statute is ambiguous on unlicensed spectrum.

“At several points, the Spectrum Act appears to contemplate that all reallocated spectrum will be licensed and auctioned. . . . On the other hand, the Spectrum Act also states that we may permit the use of such guard band for unlicensed use,” Pai said at the meeting. “If we must comply with the license and auction requirement, are there other means to encourage flexible, unlicensed use of the guard band?”

Eshoo, a member of the House Energy and Commerce Committee, wrote to Pai that the legislation was clear in its intent “to achieve a balanced spectrum policy recognizing that both licensed and unlicensed spectrum in the television band maximized the economic benefits of wireless broadband.”

“Contrary to your assertion, the legislation specifically gave the FCC the discretion to create guard bands out of spectrum that is relinquished by broadcasters, without any requirement to auction such guard bands,” she added in her letter last week.

A Pai spokesman responded that unlicensed spectrum is “an important component of a responsible spectrum strategy.”

All the FCC commissioners agree that unlicensed spectrum is a valuable resource for technologies as diverse as garage-door openers and Wi-Fi hot spots. But Republican members of the agency are urging an approach that makes as much spectrum available as possible for sale to wireless carriers such as AT&T and Verizon.

FCC Commissioner Robert McDowell, the senior Republican on the panel, said at the same meeting that the agency should consider whether the current allotment sizes of 5 MHz channel blocks “would result in a band plan that reserves too much spectrum for unlicensed uses contrary to what Congress intended.”

For his part, FCC Chairman Julius Genachowski, a Democrat, favors unlicensed bands, saying they drive economic growth and innovation. The divide suggests that much of what happens with unlicensed spectrum could depend on which party is in control of the White House after the November elections, should a vacancy come up at the FCC.

Lawmakers are watching closely as the debate unfolds at the agency, and more of them are likely to weigh in as the FCC works toward implementing the auctions in 2014. The Congressional Budget Office estimates that spectrum licenses will generate $15 billion for the government over the next decade, but Pai said some money may be left on the table if the agency doesn’t license as much spectrum as possible.

Pai is likely to find supporters on Capitol Hill. Greg Walden, R-Ore., chairman of the House Energy and Commerce Communications and Technology Subcommittee, introduced a bill during the auction legislation negotiations that would have prevented the FCC from setting aside additional airwaves for unlicensed use. Walden has not responded directly to Pai’s comments.

But John Bergmayer, a senior staff attorney for Public Knowledge, a group that favors unlicensed spectrum, said lawmakers such as Eshoo — who represents part of Silicon Valley and technology companies that stand to benefit from the availability of unlicensed spectrum — are likely to continue pushing back against proposals to limit it.

“There’s certainly always that risk that the FCC won’t have enough spectrum set aside for unlicensed use, but I’m pretty confident based on what they have proposed that they recognize its importance,” Bergmayer said in an interview.

While lawmakers are certain to make their opinions on the matter known, Free Press Policy Director Matt Wood, who monitors spectrum policy, said that’s likely to be as far as legislators go.

“It’s unlikely the Congress will do anything else,” Wood said. “It’s handed the FCC the authority to set aside spectrum for unlicensed use as the auction takes place. It’s simply trying to remind the FCC of that purpose.”