A small provision in last year’s Federal Aviation Administration authorization threatens to complicate government issuance of airman’s certificates to commercial airline pilots.

Former House Transportation and Infrastructure Chairman John L. Mica, R-Fla., insisted on including language in the 2012 bill (PL 112-95) that requires biometric eye and fingerprint data from recipients of airman’s certificates to be gathered and stored.

While the security upgrade had its share of champions, the nation’s largest pilots union opposed the new requirement. The Air Line Pilots Association argued it was unnecessary because pilots were already required to verify their identities and employment status to get certified.

But John Allen, the FAA’s director of flight standards service, told the House Oversight and Government Reform Subcommittee on Government Operations in June that the new law couldn’t have come at a worse time for the agency.

The FAA was just wrapping up rule-making mandated by 2004 anti-terrorism legislation (PL 108-458) that requires photographs to be taken as part of an airman’s certification. Current rules require pilots to carry government-issued identifications in tandem with their certificates.

Because the rule-making process related to the 2004 law was already in progress, regulators “did not contemplate those additional features” that were part of the 2012 FAA authorization, Allen said.

He said the process could be further complicated “if pilot certificates with embedded biometrics are intended to permit airport access or increase security,” because the agency would then need to improve its coordination with Homeland Security officials and the Transportation Security Administration.