The cause of the fire, which began shortly after midnight and took several hours to bring under control, was not immediately known.
A Justice Ministry spokesman said police were investigating allegations by detainees that guards had initially not taken reports of a fire seriously, causing panic among the prisoners.
"We were kept locked up. Our throats were hurting. We were kicking and screaming," an unnamed prisoner told Dutch television.
The fire raged through about a dozen two-person cells in the complex of prefabricated units.