Hobby Lobby is agreeing to hand over more than 5,000 ancient Iraqi artifacts that were allegedly smuggled, in a settlement announced Wednesday by the Justice Department.

In 2010, Hobby Lobby's president personally cut a deal to purchase "over 5,500 Artifacts, comprised of cuneiform tablets and bricks, clay bullae and cylinder seals, for $1.6 million," according to a press release from the DOJ.

The government said the arts-and-crafts retailer ignored numerous "red flags" about the artifacts.

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DOJ said the company had been "warned" by one expert that buying such a collection contained a risk that items may have been taken illegally from Iraqi archaeological sites.

"The acquisition of the artifacts was fraught with red flags," the DOJ wrote. "For example, Hobby Lobby received conflicting information where the Artifacts had been stored prior to the inspection in the UAE.

"Further, when the Artifacts were presented for inspection to Hobby Lobby’s president and consultant in July 2010, they were displayed informally."

According to the Justice Department, the shipments of thousands of artifacts arrived from dealers in Israel and the United Arab Emirates with labels that "falsely and misleadingly described their contents."

Five of the shipments were intercepted by U.S. Customs and Border Protection (CBP) in 2011.

Hobby Lobby will pay a $3 million fine and work to strengthen its practices regarding purchase of "cultural property." It will also "submit quarterly reports to the government on any cultural property acquisitions for the next eighteen months."

“We should have exercised more oversight and carefully questioned how the acquisitions were handled,” said Steve Green, Hobby Lobby's president, in a statement.

“Hobby Lobby has cooperated with the government throughout its investigation, and with the announcement of today’s settlement agreement, is pleased the matter has been resolved.”

The company said it began acquiring historic religious artifacts to preserve them for future generations and to provide access to scholars.

"The Company was new to the world of acquiring these items, and did not fully appreciate the complexities of the acquisitions process. This resulted in some regrettable mistakes," according to the statement.

"The Company imprudently relied on dealers and shippers who, in hindsight, did not understand the correct way to document and ship these items. However, since learning of these errors, the Company has been an active participant with the government’s investigation and supports its efforts to protect the world’s ancient heritage.

"At no time did Hobby Lobby ever purchase items from dealers in Iraq or from anyone who indicated that they acquired items from that country," the statement added.

The company is behind a project to build the Museum of the Bible, which will reportedly open in Washington later this year.

Hobby Lobby, an arts-and-crafts chain, famously challenged the Obama administration's birth control coverage mandate, winning its case in 2014 at the Supreme Court.

This story was last updated at 8:14 p.m.