Video clips shared by the coastguard on Wednesday night showed the vessel engulfed in flames and people being pulled out of the water into rescue boats.
The cause of the fire remains under investigation, the coastguard said.
The coastguard said preliminary interviews with the survivors suggest the fire started in the cargo hold, which is the compartment where containers and or goods are stored, the coastguard said. Some passengers were not wearing life vests, they noted.
Forty-three people have been rescued but it is unclear how many have sustained injuries.
Seven of the survivors were taken to a hospital in Culion, a larger neighbouring island, which has higher bed capacity and more comprehensive healthcare services.
A first responder told the BBC they had never seen such a disaster in Coron, calling it “really heartbreaking”.
“I was one of the people who carried and transported the casualties to the hospital last night,” they said, adding that the ferry was an hour away from its destination.
The survivors were taken to an evacuation centre in Barangay Turda, which sits just north of Marcilla. The state of their injuries is unclear.
Anelyn Magbanua is among those anxiously waiting for news of their loved ones.
Her husband Marlon had spent a few days in Manila visiting their two children, who were going to school in the capital city.
Magbanua last heard from him while the ferry was passing through a village about two hours from the port in Coron, she tells the BBC.
“I was expecting that the ferry will arrive at the pier at between 18:00 and 19:00 yesterday,” she said, adding that she had gone to bed early but was awakened by a cousin who told her the ferry Marlon was on had caught fire.
“I couldn’t describe what I am feeling right now. I have been crying and praying since last night,” Magbanua says.
She’d travelled to a hospital in Coron, hoping to find Marlon among the survivors – but he remains unaccounted for.
“My two-year-old son and I are outside the hospital as we speak. We have nothing but ourselves,” she says.
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