WASHINGTON — The Obama administration announced Tuesday that it would prosecute in civilian court a Somali accused of ties to two Islamist militant groups. The decision to fly the man to New York for trial, after interrogating him for months aboard a United States naval vessel, is likely to reignite debate about the detention and prosecution of terrorism suspects.

In an indictment unsealed in the Southern District of New York, the Somali, Ahmed Abdulkadir Warsame, was charged with nine counts related to accusations that he provided support to the Shabab in Somalia and Al Qaeda in the Arabian Peninsula, in Yemen. Mr. Warsame, believed to be in his mid-20s, was captured on April 19, and a plane carrying him arrived in New York City around midnight Monday night, officials said.

While the Justice Department called Mr. Warsame a “Shabab leader,” it does not accuse him of plotting any specific attack. Officials gave conflicting accounts of his significance: one portrayed him as a “senior operational commander” while another played down his role, saying that his capture was instead important because he had provided large amounts of intelligence about the groups and ties between them.

Regardless, his case is likely to have outside significance in the political arena because it resonates with intense debates surrounding the administration’s counterterrorism policies — including whether to bring newly captured detainees to the military prison at Guantánamo Bay, Cuba; whether to prosecute terrorism cases in civilian court or before a military commission; and what rights terrorism suspects have during interrogation.