The Sudanese woman freed from death row has been accused of trying to leave the country with fake documents, her lawyer has told the BBC.
Meriam Ibrahim was detained on Tuesday, a day after a court released her, annulling the death sentence imposed on her for renouncing the Islamic faith.
Mrs Ibrahim had emergency travel documents issued by South Sudan when she was detained at Khartoum's airport.
Mrs Ibrahim had reportedly planned to travel to the US with her family.
She was sentenced in May to hang for renouncing Islam, sparking an outcry at home and around the world.
She gave birth to a girl while on death row.
Sudan's appeal court overturned the conviction on Monday.
The US says it is working with Sudan to ensure Mrs Ibrahim, 27, is freed.
She was detained along with her husband, Daniel Wani, a US citizen, and their two children.
Mrs Ibrahim's lawyer, Elsherif Ali, told the BBC that Sudan's National Security and Intelligence Authority had lodged the complaint against Mrs Ibrahim, accusing her of obtaining a fake travel document.
Mrs Ibrahim is being held at a police station in Khartoum, Sudan's capital, he said.
South Sudan's embassy in Khartoum says the travel documents are genuine - her husband is a Christian originally from South Sudan.
Mrs Ibrahim's husband and children are believed to be staying at the embassy after being released, reports the BBC's Mohamed Osman from Khartoum.
"We are worried; that's why we want to get out of here as soon as possible," Mr Wani told AFP news agency.
But with Sudan's intelligence agency now involved, Mrs Ibrahim's case is likely to be more difficult and complicated to resolve, our correspondent says.
Earlier, Sudanese foreign ministry official, Abdullahi Alzareg, said that Mrs Ibrahim was Sudanese and should not have been using another country's travel document, stamped with a US visa.
"She came to the airport in an American embassy car - which was bullet proof and heavily guarded," Mr Alzareg told the BBC's Newshour programme, describing this as "fishy".
"Everyone knows she is Sudanese. We know she is Sudanese... imagine a British citizen trying to travel wherever, appearing at the airport carrying an emergency document from Costa Rica. This is a violation of immigration law anywhere in the world," he said.
Mrs Ibrahim would be asked to apply for a passport and exit visa on her release, Mr Alzareg said.
Sudan has a majority Muslim population, and Islamic law has been in force there since the 1980s.
Born to a Muslim father, Mrs Ibrahim married Mr Wani in 2011.
Even though Mrs Ibrahim was brought up as an Orthodox Christian, the authorities considered her to be a Muslim because that is the religion of her father.