The decision to shut down the Office of Personnel Management's electronic system for processing government background checks, and its return to paper questionnaires, has effectively frozen the issuance of new security clearances and could create a larger backlog of people waiting to be cleared to work for the federal government, some lawmakers and contractors warn.

OPM's Electronic Questionnaires for Investigations Processing system, or e-QIP, has been offline since June 29, when OPM determined that the web-based platform was vulnerable to hacking. OPM determined that agencies could have potential employees or contractors fill out the lengthy questionnaire on paper to meet deadlines for initiating background investigations.

But that step only allows only a few options. It's possible that employees who don't interact with any sensitive information could begin working, or the small group of agencies with authorization to grant interim security clearances could start issuing those clearances, an OPM spokesman confirmed this week. Those options, however, are only available for workers needing secret-level or lower clearances.

There is no temporary way to initiate background investigations on workers needing top-secret authority while e-QIP is offline for as long as six weeks. That means potential trouble for contractors.

"[W]e are deeply concerned about the potential disruptive impacts the suspension could have on federal agencies and contractors alike," Stan Soloway, the head of the Professional Services Council, recently wrote to OPM. His group represents government contractors.

"For example, companies with contractual commitments to the government could be at significant risk of non-performance if they are unable to get the requisite number of quality employees processed for new security clearances or for renewals," Soloway wrote.

Tony Anikeeff, co-chair of Williams Mullen government contracts practice, says there will be a "level of frustration, particularly among contractors." He said OPM's move will lead to background-check delays that could cause contractors to miss deadlines or other benchmarks, which could cost them business.

For example, a mid-size contractor that is trying to ramp up to complete a project that requires a lot of employees with top-secret clearances could lose the contract, Anikeeff said.

Soloway said it could cost the federal government money if the delays prevent contractors working on a fixed-cost basis to complete their work on time. In those cases, they'd have to raise their prices and seek contract modifications, Soloway said.

The Federal Investigative Services division of OPM, which actually carries out or contracts out background investigations, reportedly receives 20,000 to 30,000 submissions weekly. According to its annual report, OPM completed more than 1 million background investigations in fiscal 2014. Although OPM will not reveal which agencies handle background investigations internally, OPM conducts 95 percent of all government workers' and contractors' investigations across "more than 100 agencies," according to the annual report.

OPM spokesman Sam Schumach confirmed that background investigations already underway would continue while e-QIP is down. If a potential employee or contractor completed the questionnaire electronically before e-QIP was taken offline, their application will continue to process.

Soloway said delays in processing paper questionnaires created backlogs that led OPM to move to e-QIP in the first place. Because the government will make limited use of the paper forms during e-QIP's suspension, the backlog will only swell.

"They're sort of taking this giant step backwards," Soloway said.

OPM's sidelining of e-QIP has stirred a debate over which method is more secure — electronic or good old-fashioned paper.

Although federal agencies have probably cut back on filing cabinets and have fewer employees used to filing paper, security-granting agents may look more closely at information written on paper, Anikeeff said.

Thumbing through hundreds of pages manually versus scrolling through them on a computer screen may make something suspicious pop out more, Anikeeff said. "I don't think there's a greater threat; I don't think any of the bad guys will sneak through the system," he said.

Pasi Eronen, a cyberexpert at the Foundation for Defense of Democracies, said the biggest issue with paper forms is whether agencies and their employees are equipped to handle physical documents.

"Are there still valid and approved processes in place for manual handling of security clearance documents?" he asked. "If so, is there still personnel in place who has actually been involved in those processes and can still do it? And even more importantly, is there enough personnel in the first place to move from the optimized, digital processing into manual processing?"

In the memo outlining the temporary procedure issued by OPM Director Katherine Archuleta and National Intelligence Director James Clapper, there were no specifics about to handle the paper forms versus electronic ones, other than directions for each agency to maintain the hard copies and to not forward on to OPM.

As for "hacking" paper documents, "the Remington typewriter has become the novel way to keep things secure," Anikeeff offered. "My concern is it would get lost more than stolen."