Malaysian Maritime Enforcement Agency director-general Admiral Datuk Mohd Zubil Mat Som tweeted that the four missing were found at about 11.25am.
Earlier in the morning, the Dayang Topaz with more than 100 crew members on board sunk in northern Sarawak after running into trouble.
A massive search-and-rescue operation was launched after distress signals from the ship were picked up.
Following that, the MMEA confirmed that 121 people had been rescued.
It said the Maritime Rescue Coordination Centre in Putrajaya received a report on Dayang Topaz being in trouble from the crew of another ship named Sapura Construction.
"At 6.45am, Sapura Construction received distress signals from another ship Dayang Topaz about 7.7 nautical miles offshore Kuala Baram in Miri.
"Sapura Construction crew rushed to the site. They saw Dayang Topaz sinking.
"MMEA sent our ships along with those from Petronas and Shell. They found 125 crew members had jumped into the sea from the sinking ship.
"By 8.45am, 121 crew members had been rescued.
At the time, four crew members were still missing.
Northern Sarawak has been battered by strong winds and heavy rain in the past two days. The ship is believed to have been hit by massive waves.
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