The alleged transgressions are so serious that a federal watchdog indicated he plans to recommend that the Office of Personnel Management, which oversees most background checks, end ties with USIS unless it can show it is performing responsibly, the Washington Post quoted its sources as saying.
Cutting off USIS could present a major logistical quagmire for the nation's already-jammed security clearance process.
"The federal government relies heavily on contractors to approve workers for some of its most sensitive jobs in defence and intelligence," the report said.
Explaining the laxes, the report said that after conducting an initial background check of a candidate for employment, USIS was required to perform a second review to make sure no important details had been missed.
"From 2008 through 2011, USIS allegedly skipped this second review in up to 50 per cent of the cases. But it conveyed to federal officials that these reviews had, in fact, been performed," it said.
Snowden, 30, had blown the lid off National Security Agency's secret spy programme and is charged with violating American espionage laws. He is currently in Russia after fleeing from Hong Kong.
The documents revealed the existence of programmes that collect records of domestic telephone calls in the US and monitor the internet activity of overseas residents.
The disclosures shook the US intelligence community and raised questions about whether the NSA is eroding American civil liberties.
Snowden is charged with theft of government property, unauthorised communication of national defence information and wilful communication of classified communications intelligence.
Snowden has applied for asylum in Ecuador. The US has revoked his passport.
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