Kseniia Petrova, a Russian-born Harvard scientist, has been charged with smuggling biological material into the United States — an escalation in a case that has already raised legal and civil rights questions over her detention.

Federal prosecutors allege that Petrova, 30, violated U.S. customs law by failing to declare preserved frog embryos in her luggage when she arrived at Boston Logan International Airport on Feb. 16 from Paris. She now faces a charge of smuggling goods into the United States.

According to a criminal complaint filed under seal this week and made public on Wednesday, a CBP canine alerted officers to Petrova’s duffle bag, which was later searched. Officers found clawed frog embryos, paraffin slides and other samples.

When first questioned, Petrova “denied carrying any biological material,” the affidavit says. After being shown a message from her phone advising her to “make sure you get the permission etc. like that link I sent to leon-/group chat about frog embryos because TSA went through my bags at customs in Boston,” she acknowledged the samples. Asked whether she knew they had to be declared, she responded that she “was not sure.”

Petrova described the incident differently.

“They asked if I have any biological samples in my luggage. I said yes,” she previously told NBC News from detention in Louisiana. She described confusion over the customs procedures and a lengthy interrogation by Customs and Border Protection officers.

“Nobody knew what was happening to me. I didn’t have any contact, not to my lawyer, not to Leon, not to anybody,” she said, referring to Dr. Leon Peshkin, a principal research scientist at Harvard’s Department of Systems Biology and her manager and mentor. “And the next day, they didn’t say what would happen. I was waiting in a cell.”

The document notes that Petrova told Customs and Border Patrol officers that she had protested against the Russian Federation and expressed fear about returning. She asked to go to France, where she held a valid Schengen visa, but was instead later taken into ICE custody where she remains detained at Richwood Correctional Center in Monroe, Louisiana.

During a habeas hearing Tuesday in Vermont federal court, U.S. District Judge Christina Reiss questioned the legality of the government’s actions. “Where does a Customs and Border Patrol officer have the authority on his or her own to revoke a visa?” she asked. “I don’t see anything about a customs violation.”

Petrova’s attorney, Gregory Romanovsky, argued that the government acted beyond its authority. “There is no corresponding ground of inadmissibility,” he said. “You cannot be found inadmissible because of the customs violation.”

“She was willing to go to Paris, but the government did not let her,” Romanovsky added.

Reiss scheduled a tentative bail hearing for May 28 and asked for further briefing on whether the court has jurisdiction to release Petrova.