The Dutch coastguard and navy and other ships plucked 13 survivors from the water after the Baltic Ace, a 23,000 tonne car carrier, collided with container ship the Corvus J at around 7.15pm Wednesday (5.15am AEDT Thursday) about 100km southwest of Rotterdam.
The Baltic Ace sank shortly afterwards, the coastguard said. The Corvus J was also damaged, but assisted in the search for missing crew, according to Dutch media reports.
"We have suspended the search until first light," Coast Guard spokesman Peter Verburg told AFP at 3am.
"The chances of finding them alive are slim," he added, saying there was a chance that some of the crew may have gone down with the stricken vessel.
Another Coast Guard spokesman Marcel Oldenburger told AFP earlier that 13 crew members who were all on board the 148m Bahamas-registered Baltic Ace had been rescued.
Four survivors were flown to a hospital in Rotterdam, seven taken by rescue helicopter to a hospital in Belgium and two were being treated on board a ship that found them, Oldenburger said.
"They are all in shock" and are believed to suffer from hypothermia, he said, but their lives were not in danger.
With weather conditions over the North Sea worsening including some snow flurries and the temperature dropping, hopes of finding survivors "were diminishing", Oldenburger said.
He added strong winds and waves of up to 3m also had hampered the rescue operation.
At least three helicopters - one of which was fitted out with infrared imaging equipment to search in the darkness - and a plane joined the search, but no crew were spotted since a fourth body was discovered in the water.
The Baltic Ace was under way from Zeebrugge in Belgium to Kotka in Finland and the Cypriot-registered Corvus J from Grangemouth in Scotland to Antwerp in Belgium, according to shipping tracker website MarineTraffic.com.
"At this stage we don't know what caused the accident," said Verburg: "Our first priority right now is the safety of the crew."
The shipping lane where the accident happened is one of the busiest in the North Sea and an important passing point for ships sailing into Rotterdam port, Europe's largest and the fifth-largest in the world.
Rotterdam port spokesman Sjaak Poppe told AFP the collision would not affect shipping in and out of the port.
In one of the most serious collisions in Dutch waters in recent years, the Greek crude oil tanker Mindoro in October 2010 collided with the container ship Jork Ranger off the coast of Scheveningen near The Hague, spilling thousands of litres of kerosene (jet fuel) into the sea, the European Maritime Safety Agency said on its website.
