The crew member, who was found drifting in a life jacket, said the ship had capsized.
The Gulf Livestock 1 sent a distress signal from the East China Sea after being caught up in Typhoon Maysak.
The search for the rest of the crew and ship continues but has so far failed to find any more survivors.
The crew of the freighter includes 39 seamen from the Philippines, two from New Zealand and two from Australia.
What happened to the ship?
According to the Japanese coastguard, the man rescued is one of the Filipino crew, who said the ship’s engine failed before it capsized after being hit by a wave.
Eduardo Sareno, the vessel’s 45-year-old chief officer, said the crew had been instructed to put on lifejackets and that he jumped into the water.
He said he did not see any other crew members before he was rescued.
Mr Sareno’s wife told the BBC he’d spoken to her from a hospital telling her he was safe.
The Gulf Livestock 1 left New Zealand on 14 August headed for China, with the journey expected to take 17 days, New Zealand’s foreign ministry said.
On Wednesday night, the ship sent a distress call from waters to the west of Amami Oshima island in south-western Japan.
The Philippine department of foreign affairs said its consulate in the Japanese city of Osaka was “monitoring the situation and co-ordinating” with authorities.
The Japanese coastguard “is launching a second search-and-rescue mission prior to the expected incoming typhoon”, it said in a press release.
Liezel Pitogo, 38, last spoke to her husband Lindon, a seafarer on the ship, on Tuesday evening.
He said they were travelling to China but were a bit worried about the weather, she told the BBC, speaking from Quezon province in the Philippines.
“His phone was unreachable on Wednesday,” Ms Pitogo said. “I thought it’s just a problem with the erratic signal when they are on the sea but I saw a Facebook post from a seaman’s wife about a cargo ship that went missing so I started contacting and asking some of the other wives.”
Both Australia and New Zealand said they were providing consular assistance to the families of their crew members.
The Gulf Livestock 1 is a 139m (450ft), Panamanian-flagged cargo vessel built in 2002.
Strong winds and torrential rains from the typhoon battering the region are hampering the search effort.
How powerful is the typhoon?
At least two people are reported to have been killed in the city. One was a woman whose apartment window was shattered by the force of the wind.
Another man in Busan was believed to have fallen to his death from the roof of his house. Yonhap news agency reported he had been repairing a leak.
More than 2,200 people have been evacuated to shelters and about 120,000 homes were left without power in the affected region. Wind and rain have flooded Busan’s streets.
Flights have been cancelled and ferries suspended. Maysak is one of the strongest storms to hit the region in years. It is moving north and made a second landfall at Kimchaek in North Korea, before weakening as it tracked into north-east China.
North Korean TV showed flooded farmland.
The storm comes after the Korean peninsula suffered a summer of monsoons and widespread flooding. Another typhoon – Haishen – is forming south of Japan and is due to hit the Korean coast on Monday.