YOKOTA AIR BASE, Japan — It was a rare situation: two of the Navy’s largest warships parked within several miles of each other in Yokosuka harbor.

Though similar in appearance and function, there’s a distinct difference between the aircraft carriers USS Carl Vinson and USS Kitty Hawk.

Two nuclear reactors on the Vinson convert water into steam to power the 100,000-ton ship. On the Kitty Hawk, about 10,000 tons smaller than its sister ship, fossil fuels generate steam for electricity.

For the sailors aboard the nuclear supercarrier, it’s a subtle difference. The air on the ship is cleaner, they say, since smokestacks don’t spew burning diesel fuel. Otherwise, they don’t think much about living above a nuclear power plant, sometimes thousands of miles from shore.

But in Japan — the only nation to suffer an atomic bombing — the presence of a nuclear warship in one of its main harbors is a sensitive issue.

Hundreds of Japanese protesters greeted the arrival last week of the Vinson and members of its battle group at Yokosuka Naval Base. The carrier, the USS Antietam and USS Ingraham made their first port call in Japan after deploying to the Western Pacific as a deterrent. But questions of nuclear-carrier safety were raised several times onboard the Vinson, when local reporters spent a night on the ship last week as it steamed toward port.

“If it were dangerous, do you think I would be doing it and subject all these folks to it? Absolutely not,” Capt. Richard Wren, who assumed command in October 2001, told the Japanese reporters.

Navy officials at Commander, Naval Forces Japan, headquartered at Yokosuka, point to the nuclear carrier fleet’s flawless safety record.

Of the Navy’s 12 active carriers, nine are powered by nuclear reactors.

“There’s never been a nuclear accident in 48 years of the Navy’s program,” said CNFJ spokesman Jon Nylander.

Wren and Rear Adm. Marty Chanik, commander of Carrier Group 3 — the Vinson’s battle group — say they prefer the nuclear-powered carriers to the conventional ones.

Nimitz-class nuclear carriers such as the Vinson can steam more than 20 years before “refueling.” A conventional carrier such as the Kitty Hawk has to refuel every three to five days, Chanik said.

Without that fueling requirement, nuclear carriers can relocate rapidly and travel long distances at high speeds without worrying about fuel-burn rates. Fuel is stored aboard the ship for the air wing.

Petty Officer 1st Class Alberto Melendez, an aircraft director on the Vinson, said the cleaner air makes a huge difference.

“I’ve been on two conventional carriers before, and this is my second nuclear carrier,” he said. “Life is good. You can breathe a lot better up here, you don’t have exhaust and it’s a lot quieter.”

Strategically, the nuclear carrier has another advantage: “We’re not as easily spotted. The conventional carrier leaves a big ol’ track of black smoke wherever it goes,” Melendez added.

Marine Corps Staff Sgt. Patrick Smith, assigned to Marine Fighter Attack Squadron 314 deployed with the Vinson, said he never understood why some Japanese made such an issue about nuclear carriers until talking with his buddy recently.

“He said, ‘If what happened to the Cole happened to us, there would be a whole lot of dead people really quick,’” Smith said, referring to the terrorist bombing of the USS Cole in October 2000, when the ship made a refueling stop in Yemen. Seventeen sailors died in the attack.

“Besides that, it’s not that big of a deal,” Smith said.

Wren pointed out that Nimitz-class carriers are designed “to be taken into combat operations” with an appropriate level of engineering and shock resistance.

“All of that engineering translates into additional safety,” he said.

— Joseph Giordono contributed to this report.