The Gulf Livestock 1 was carrying 6,000 cows and 43 crew members when it went missing on Wednesday after being caught up in Typhoon Maysak.
Japanese officials said a 30-year-old Philippine national became the ship’s second known survivor when he was found drifting on a life raft on Friday.
Another man was found in the water hours earlier but pronounced dead.
The vessel’s chief officer, Eduardo Sareno, was rescued on Wednesday evening.
The crew of the freighter included 39 people from the Philippines, two from New Zealand and two from Australia.
Hopes of finding more survivors were fading on Friday as a new powerful storm, Typhoon Haishen, barrelled towards the area.
What do we know about the survivors?
The Japanese coastguard said the second survivor is a 30-year-old Philippine national, who was working as a deckhand on the ship.
He was wearing a life jacket and floating in a raft when rescuers discovered him on Friday. Officials said he was conscious and able to walk unassisted.
The first survivor of the accident, 45-year-old Mr Sareno, was found late on Wednesday.
“I’m the only one?” he asked rescuers after being pulled from the water.