The U.S. military reconfigured the USS Ponce, commissioned in 1971, to serve as an advanced Navy control center. Its crew of 55 Navy sailors and 120 civilian mariners supports the U.S. Navy's 5th Fleet, which is stationed in Bahrain.
Hagel said from Manama the USS Ponce represents "the future of our naval operations."
Hagel arrived Thursday in Bahrain to take part in the so-called Manama Dialogue. He first visited Bahrain in 2004 to take part in the conference when he served in the U.S. Senate.
The defense chief said he'd make strategic commitments to regional allies during a series of meetings in Bahrain during the next few days.
"I will assure our partners that we're not going anywhere," he was quoted by the Pentagon's news service as saying Friday.
The U.S. government has been accused of placing its strategic interests in Bahrain above concerns over the country's human rights record.
The British government this week issued a travel advisory for Bahrain, warning of the possibility for violent demonstrations.
More than 100 people died during anti-government demonstrations in Bahrain in 2011. The government has been accused of taking a harsh stance against its opponents.