"Any decision to end a search is painful," Capt. Mark Fedor said earlier, adding of the El Faro crew, "We've been baptized in the same salt waters."
Search crews are confident they "did all they could in this search effort," Fedor said. Thirty-three people were on board El Faro. One body was found in the water Sunday, the Coast Guard has said.
Two family members who had relatives aboard the container ship that went missing amid Hurricane Joaquin last week told CNN that the Coast Guard had informed them of the decision Wednesday afternoon.
The president of the company that owns the 790-foot long, 40-year-old ship pledged to help those affected by the tragedy.
"While the search might be over, our support and commitment to the families and loved ones and friends of those on board has not ended nor will it," Tote Incorporated President Anthony Chiarello said.
The National Transportation Safety Board has requested that a salvage unit of the U.S. Navy head to the search site to undertake underwater surveying, a source close to the investigation told CNN.
Fedor described the search effort to reporters, saying it involved hurricane hunter aircraft flying into the eye of the 140-mph storm at 10,000 feet last Thursday and Friday and planes battling 100-mph winds Saturday, pushing the aircraft "to the extent of their operating limits."
Crews have honed the search area down to two debris fields -- one of about 345 square miles near the El Faro's last-known location (36 miles to the northeast of Crooked Island in the Bahamas) and one of about 81 square miles located roughly 69 miles north of that position.
He said search crews would have focused on anything indicating that there were survivors, and he believes the crews would have found a life boat or life raft if one were out there. Crews did find a deflated raft and personal flotation devices, he said.
"We do think (the El Faro is) near that last-known position," Fedor said.
The source close to the investigation told CNN that the ship's two life boats were not enclosed (like newer models) and that would have affected the crew's ability to survive in extremely rough seas.
Among the vehicles taking part since Sunday were helicopters, Coast Guard and Air Force HC-130s making low passes over the water, a Navy P-8 flying at 27,000 feet, commercial tugboats and three Coast Guard cutters: the Northland, the Resolute and the Charles Sexton.
Personnel not normally involved in search operations -- including cooks and engineers -- could be found on the ships' bridges peering through binoculars and night-vision goggles in hopes of finding the ship.
CNN witnessed this to a degree, first hand, on Monday when the Coast Guard took two CNN journalists up for a 10-hour flight
northeast of San Salvador Island, Bahamas. Every crew member -- including the navigator, pilots, maintenance technicians, electrical technicians and the engineer -- were involved in the search for the full flight, which covered more than a 1,000 square miles.
The recovery mission will now focus on the voyage data recorder, according to Bella Dinh-Zarr, vice chairwoman with the National Transportation Safety Board, which is leading in the investigation.
The recorder, a Voyage Master II manufactured by Sperry Marine, captured onboard audio from the bridge and the ship's course and speed. It's capable of surviving at the depths to which the El Faro is feared to have sunk, she said and would've begun pinging once it was submerged in water. It has a battery life of 30 days, Dinh-Zarr said.
The NTSB has remotely operated underwater vehicles that will be able to retrieve the recorder once it's located, she said.
News that the search was reaching an end came after a friend of the captain told CNN that Michael Davidson was a capable and experienced mariner who likely believed he had a good plan to avoid Joaquin when he and 32 other crew members departed Florida for Puerto Rico last week.
"My guess is that he saw that he could outrun the storm, providing everything went right," Larry Legere, of Maine, said of Davidson.
But the ship's main propulsion failed, the ship's owners say, stranding the crew in the path of the storm -- and the Coast Guard believes it sank.
Authorities have found debris
, but have not seen the ship nor any survivors since the cargo vessel lost contact near the Bahamas on Thursday -- just as Hurricane Joaquin was churning through the area.
Ship owners: Captain considered his route safe
The owners of El Faro insist the captain had a "sound plan" to avoid Hurricane Joaquin -- a plan that only unraveled when the ship's main propulsion stopped working.
The captain had real-time weather information when he left the port in Jacksonville and reported favorable conditions at the outset, Tote Services President Phil Greene told reporters.
Given the weather system, the captain's "plan was a sound plan that would have enabled him to clearly pass around the storm with a margin of comfort that was adequate in his professional opinion," Greene said.
But knowing that a potential hurricane was brewing, why was El Faro allowed to go ahead with its scheduled route?
Tote officials said they trust the company's captains to be the decision makers, and that up until El Faro lost its propulsion, the reports were not alarming.
The captain sent an email to headquarters September 30 saying he was aware of the "weather condition" -- the increasingly powerful Hurricane Joaquin -- and that he was monitoring its track, though conditions where the ship was "looked very favorable," Greene said.
But the next day, El Faro lost propulsion right in the path of the hurricane, Fedor said.
"They were disabled right by the eye of Hurricane Joaquin," Fedor said Tuesday.
"If they were able to abandon ship and put on their survival suits, they would have been abandoning ship into that Category 4 hurricane. So you're talking about 140-mile-an-hour winds, 50-foot seas, zero visibility. It's a very dire situation, a very challenging situation even for the most experienced mariner."
What happened to the ship's propulsion?
The captain told his company that El Faro was disabled, but "did not explain in his communication why he had lost propulsion," Greene said. "He indicated that he had had a navigational incident."
The captain had said the ship was listing, or leaning, 15 degrees.
Fedor said there was a report that a scuttle -- a hatch in the deck of the ship -- had been open and water had gotten in.
"I'm not certain of the circumstances, why it was open," he said, responding to a question from CNN. "But that's where the water came from and caused the 15-degree list."
It was also unknown how much time lapsed between the time the propulsion failed and the time the captain reported the problem to his bosses.
"Based on evaluating the position of the ship when the captain reported (the propulsion failure), he was in the path of the storm," Greene said.
"I think what is regrettable on this is the fact that the vessel did become disabled in the path of the storm, and that is what (ultimately) led to the tragedy."
NTSB investigators arrived in Jacksonville on Tuesday.
"Our mission is to understand not just what happened, but why it happened, and to issue recommendations and findings to prevent this from happening again," Dinh-Zarr said.
Captain's friend: 'He would have weighed all of the factors'
Legere told CNN's "New Day" that he's known Davidson since the 1970s, when Legere was a ferry captain and Davidson served as a deck hand.
Davidson worked his way up, was promoted to captain and eventually attended Maine Maritime Academy, Legere said.
"Mike was a very capable and experienced captain," Legere said. "He would have weighed all of the factors -- the weather, the condition of the ship."
Legere said that deadlines to deliver cargo generally play into a captain's decision to sail.
"However, I don't believe he would have been pressured by the company, considering the weather forecast and so forth," he said.
Correction: A previous version of this story incorrectly identified Jordan Dehlinger as an El Faro crew member. In fact, her boyfriend, Dylan Meklin, was aboard the ship, according to CNN affiliate WMTW and the Portland Press Herald. Andrew Dehlinger is Jordan's father.