The Department of Justice says thousands of cuneiform tablets and clay bullae, originally from Iraq, were smuggled into the United States via the United Arab Emirates and Israel in packages shipped to the Oklahoma-based company.
Hobby Lobby said that in 2009 it began acquiring artifacts "consistent with the company's mission and passion for the Bible" with the goal of preserving them for future generations and sharing them with public institutions and museums.
US prosecutors said the company was warned against the risk of such items being looted from archaeological sites in Iraq and that improper declaration of country of origin could lead to forfeiture.
But in December 2010, Hobby Lobby agreed to pay USD 1.6 million for more than 5,500 artifacts, including cuneiform tablets, clay bullae and cylinder seals.
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The company did not communicate with the dealer who purportedly owned the artifacts and instead wired payment to personal bank accounts held in the names of other people, federal prosecutors said.
In 2011, the firm also received a package of 1,000 clay bullae shipped by an Israeli dealer and accompanied by a false declaration stating that the contents originated in Israel.
"American collectors and importers must ensure compliance with laws and regulations that require truthful declarations to US Customs and Border Protection," said acting US attorney in Brooklyn, Bridget Rohde.
Hobby Lobby agreed to forfeit the artifacts, as well as 144 cylinder seals and an additional sum of USD 3 million to settle the civil action, prosecutors said.
"We should have exercised more oversight and carefully questioned how the acquisitions were handled," said company president Steve Green.
Hobby Lobby calls itself the largest privately owned arts-and-crafts retailer in the world with approximately 32,000 employees and operating in 47 states.
In 2014 the US Supreme Court ruled in favour of Hobby Lobby and another corporation, allowing them to refuse contraceptive coverage to female employees on religious grounds.