A 16-year-old boy has been charged with murder and aggravated sexual abuse in Florida in the 6 November death of his 18-year-old stepsister on a Carnival cruise ship, the US justice department said Monday.

Timothy Hudson was initially charged in February and subsequently indicted on 10 March. But the breadth of the case was not known until a seal was lifted Friday, weeks after US district judge Beth Bloom in Miami said he would be prosecuted as an adult at the request of the government.

Anna Kepner, Hudson’s stepsister, had been traveling on the Carnival Horizon ship with her family. Before the ship was scheduled to return to Florida, her body was found concealed under a bed in a room she was sharing with two other teens, including the younger stepbrother.

The cause of Kepner’s death was determined to be mechanical asphyxia, which is when an object or physical force stops someone from breathing.

Email and voicemail messages seeking comment from Hudson’s attorneys about the charges were not immediately returned Monday. Hudson, whose name was disclosed through his signature on documents filed in federal court, has remained free in the care of an uncle since his arrest in February.

Kepner’s father, Christopher Kepner, released a statement, saying the family was placing “trust in the justice system to pursue the truth with care and integrity”.

“At the same time, we are deeply troubled that, despite the seriousness of the charges, he has not been taken into custody,” Kepner said. “The situation is deeply painful and complex for the entire family.”

In a written statement, US attorney Jason Reding Quiñones said, “Our hearts go out to the victim’s family during this unimaginable loss. A federal grand jury has returned an indictment charging serious offenses that allegedly occurred aboard a vessel in international waters.”

Kepner was a high school cheerleader at Temple Christian school in Titusville, Florida, about 40 miles (65 kilometres) east of Orlando. At her memorial service in November, family members encouraged people to wear bright colors instead of the traditional black “in honor of Anna’s bright and beautiful soul”.

Teens are rarely prosecuted in federal court. Hudson pleaded not guilty when he was initially charged in February, though the proceedings were not public because of his age – and neither were court documents. He was seen at the courthouse wearing a ball cap and a hoodie pulled tightly around his face.

A judge on 6 February said Hudson must wear an electronic tether while living with an uncle. The order was changed to allow him to join his father for a few days recently at a landscaping business, newly unsealed court records show.

Prosecutors objected to Hudson’s release, citing dangerousness, and asked a judge Monday to revisit that order now that he has been charged as an adult. Defense lawyers were given a week to respond.

“He committed these crimes against a victim with whom he had no apparent relational strife, and whom he was being raised to view as a sibling,” assistant US attorney Alejandra López said in a court filing.