MOMBASA, Kenya — Cheering and guarded by Navy Seals, the crew of an American ship reached a Kenyan port Saturday evening without their captain, still held hostage by Somali pirates in a lifeboat hundreds of miles from shore. Capt. Richard Phillips, 53, of Underhill, Vt., was seized Wednesday when he thwarted the takeover of the 17,000-ton U.S.-flagged Maersk Alabama, which was carrying food aid for people in Somalia, Rwanda and Uganda.

Crew members said that as the pirates boarded his cargo ship, Phillips had ordered them to lock themselves in a cabin and surrendered himself. “He saved our lives,” second mate Ken Quinn, of Florida, declared from the ship as it docked in the resort and port city of Mombasa. “He’s a hero.”

The crew later overpowered some of the pirates, but the Somalis fled with Phillips to an enclosed lifeboat. Quinn told reporters the experience was “terrifying and exciting at the same time.”

The president of the company that owns the Maersk Alabama called the ship a crime scene and said crew members had to remain aboard while the FBI investigates; crew members were provided phones so they could stay in touch with family. Under U.S. law, crimes aboard U.S. ships or against American citizens can be prosecuted in U.S. courts, even when they occur in international waters.

U.S. military officials said Saturday the pirates in the lifeboat, believed to be armed with pistols and AK-47s, fired a few shots at a small Navy vessel that had approached. No one was hurt, and the Navy vessel turned away. The U.S. sailors were not conducting a rescue attempt and did not return fire. Negotiations with the pirates were continuing, the Pentagon said, though few other details about them were released.

Also Saturday, NATO confirmed that an Italian tugboat was hijacked in a new attack in the Gulf of Aden off Somalia’s north coast as it was pulling barges.