WASHINGTON — A Somali citizen captured in April was interrogated aboard a U.S. warship for two months and is now in New York to face terrorism charges.

The case against Ahmed Abdulkadir Warsame is the first known example of the Obama administration’s secretly holding and questioning a terror suspect.

It shows the Obama administration is sticking by its plan to use civilian courts to prosecute terrorists, a strategy successful for years under President George W. Bush but which has drawn fire from Republicans since Obama became president.

The case also offers a glimpse at how the U.S. plans to interrogate detainees now that Obama has closed the CIA’s network of secret prisons.

The military captured Warsame on April 19, and then put him aboard a Navy warship, where he was interrogated at sea by intelligence officials, senior administration officials said Tuesday. Under interrogation, Warsame gave up what officials called important intelligence about al-Qaida in Yemen and its relationship with al-Shabab militants in Somalia. The two groups have been known to have ties, but the extent of that relationship has remained unclear.

After the interrogation was complete, the FBI began to interrogate Warsame from scratch, in a way that could be used in court. After the FBI informed him of his rights under U.S. law not to incriminate himself, to remain silent and to have an attorney, he opted to keep talking for days, helping the government build its case.

One of the unanswered questions of the Obama administration’s counterterrorism strategy has been what it would do if it captured an important terrorist. Obama doesn’t want to send more people to the Navy’s Guantanamo Bay prison used by the Bush administration, and the CIA’s “black sites” are closed.

The unusual case against Warsame was foreshadowed in congressional testimony in June when Obama’s choice to become commander of the U.S. Special Operations Command, Navy Vice Adm. William H. McRaven, told senators that the U.S. could hold suspected terrorists on naval ships until prosecutors file charges against them. McRaven did not say exactly how long such detentions could last.

The senior officials who spoke to reporters Tuesday said there are no other detainees in custody aboard ships.

Obama took office promising to end harsh interrogation tactics and close Guantanamo Bay. Congress has blocked the administration from transferring any detainees out of Guantanamo Bay for trial in the U.S., and some in Congress are also questioning whether all new terrorism cases should be handled by military commissions.