Hundreds of asylum-seekers have been bussed away from a Dutch refugee center after overcrowding at the facility led to more than 700 people sleeping rough outside its gates, many for almost three weeks.

Aid organizations had warned of a looming humanitarian emergency at the Ter Apel site near the northern city of Groningen, where overcrowding has been building for months, exacerbated by long delays in processing asylum claims.

The crisis came under the spotlight after the death of a three-month-old baby at the site, with the Dutch justice department launching a probe this week into whether negligence had played a role in the fatality. 

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As large numbers of asylum-seekers were taken away from the site to other facilities in Netherlands on Friday, there were hopes that the men could have their asylum claims processed and be given shelter while their applications were under consideration.

"Several hundred people were taken by bus late last night to other reception locations across the country," said Leon Veldt, spokesperson for the Dutch government's refugee organisation on Saturday.

"We hope to slowly normalise the situation at Ter Apel," he said.

Dutch newspapers however reported on Saturday that dozens of men remained behind at the site, mainly out of fear of losing their places in the queue.

On Friday the Red Cross and the Dutch arm of Doctors Without Borders (MSF) warned of a growing medical and humanitarian emergency. 

Earlier in the week hundreds of men had set up camp on the ground under makeshift tarpaulins near the facility, close to a row of portable toilets, but with no other facilities.

Dutch Prime Minister Mark Rutte admitted there were "shameful scenes at the center" and that mistakes had been made, but he claimed to be finding a "structural solution" to the problem.

The Dutch government late Friday announced a series of measures to deal with the crisis at the country's main migrant center, which has been blamed on staff shortages at COA and housing shortages in the Netherlands.

Many asylum-seekers whose applications have been approved were forced to remain in such sites.

One of the reasons given for the substandard processing is that there are no homes available on the Dutch market, a claim contested by pro-refugee groups. 

Instead of focusing on opening up housing the government's measures focus on trying to stop more asylum seekers coming into the country.

That includes temporarily suspending a migrant deal with Türkiye to take on 1,000 asylum seekers per year and only bringing over families of successful applicants once housing outside reception centres have been found.

The Dutch government also promised to open more centers, including the military possibly making available a property, and using a boat in Arnhem with 200 beds and accommodation at the TU Delft University.