By Larry Shaughnessy

When Navy security personnel onboard USNS Rappahannock opened fire on a small boat near Dubai on Monday, killing one Indian fisherman and injuring three others, it was the final step in an effort to protect the ship without resorting to force.

The incident is not without controversy. One of the Indian fishermen onboard the small boat told Reuters they did not get any warnings before they were fired on.

"We were speeding up to try and go around them and then suddenly we got fired at," the injured fisherman said. The U.S. military is investigating the incident.

"We certainly regret the loss of life in this incident…. There were, in fact, warning measures that were taken based on what we know now. ," said Pentagon spokesman George Little.

The incident lasted just three minutes, according to a Central Command document obtained by CNN's Security Clearance. The document illustrates how the incident escalated in a quick succession of steps.

In Navy parlance, the USNS Rappahannock is an "underway replenishment oiler,” meaning it can supply warships while they are sailing at sea.

Notice it's USNS not USS, which means it is owned by the military, but it's not a warship. It has a civilian commander or "master" and a mostly civilian crew. The only Navy sailors onboard are the security detail protecting it.

The Navy's security strategy has changed drastically since October 2000 when a small boat packed with explosives pulled up beside the USS Cole and blew up, killing 17 American Sailors and nearly sinking the destroyer.

"It's constantly on your mind," said retired Vice Adm. Pete Daly, who was in charge of a destroyer squadron when the Cole was attacked. "I would say that the Navy, as a result of the Cole, significantly reevaluated what the Navy calls the waterborne threat."

Daly said the Navy was caught off guard by the Cole attack.

"When a ship was in a harbor, we thought we were doing a very good job of the landward threat. You had gates and guards and barbed wire. But from the seaward side, not as much as we should have."

As for Monday's incident, the Department of Defense said it appears the Rappahannock's crew acted properly.

"Based on what we know now, a series of warning measures were issued to the oncoming vessel. Those warnings were not heeded. And the vessel was fired upon," Pentagon Press Secretary George Little said Tuesday.

The small boat first got the attention of the Rappahannock when it was about five nautical miles away, according to the military document. When it was about 1,200 yards from the Navy ship's starboard side (point #2 on diagram) it turned toward the Rappahannock and the ship responded by beginning the series of warning measures.

"The Navy ship will never start at direct lethal fire. There's a whole rules of engagement that occurs that has different levels," Daly said.

Daly spelled out how those warning measures work, starting with nonlethal means such as radio calls using common civilian channels, loudspeaker announcements, and flares and lights to get attention.

In the case of the Rappahannock incident, within a minute of the boat approaching, the security team "initiated first level of defensive, nonlethal warning procedures," according to the military document. The vessel was closing in and was within 900 yards but "ignored the warning and continued toward" the Navy ship.

Daly said the next level is to fire warning shots, shooting into the water ahead of the encroaching boat but without putting the boat or passengers in danger. The Rappahannock security team initiated a "next level of defensive, nonlethal procedures" one minute later, but those were ignored by the approaching boat that was just 150 yards away, according to the Central Command document.

At this point, according to Daly, the crew will fire. This occurred when the boat was just 100 yards from the Rappahannock (point #5 on the diagram), with a .50-caliber machine gun. The intent of the direct fire is not to harm people, it is to stop the approaching boat, Daly said.

But the Navy acknowledges when it opens fire on another vessel, there is a risk people could get hurt or killed. Daly said that's why direct fire is the action of last resort.

"This is a very deliberate and responsible graduated response," Daly said.

Because this was a civilian crew other than the security team, it would not have been the master of the Rappahannock who ordered the security team to open fire on the approaching boat.

In this case, the senior Naval officer leading the security team would have given the order to fire, explained Daly.

After Rappahannock opened fire, the boat "slowed for the first time and turned to port, passing astern of the Rappahannock. The Navy crew then re-initiated nonlethal procedures with the boat, which was within 90 yards of the naval vessel. The boat then stopped and the Rappahannock "goes to full speed to separate from the vessel.

Unfortunately, this kind of incident may happen again as the Navy sends more ships into the crowded Persian Gulf that is rife with tension.

When a ship's underway, coming in or out of harbors or in narrow passages" you risk having close encounters, Daly said.