"In this country, laws are made to be obeyed, and that goes for everybody," Health Minister Ab Klink said in a letter to parliament amid reports of growing resistance to the ban in the hospitality industry.
His spokeswoman, Saskia Hommes, told AFP that contravention of the ban, which came into operation on July 1, can now also be prosecuted under criminal law.
Inspectors from the health department's Food and Consumer Product Safety Authority, who have issued 500 fines for contraventions since October 1, would in future work closely with prosecutors.
"Using criminal law instead of only civil law will enable us to issue fines faster, and tougher punishments," said Hommes. "In the worst case scenario, businesses that repeatedly break the law can be closed down."
Dozens of Dutch establishments, especially smaller ones, have started putting their ashtrays out again, arguing that they were losing customers and didn't have the space or money to erect separate smoking spaces.
A group of pub owners have asked Klink to consider compensating them for their financial losses, which he reportedly refused.
A recent poll had suggested that more than half of pub and restaurant owners were considering closing shop due to the ban.
In the town of Den Bosch in the south of the Netherlands, the majority of pubs have been allowing their clients to smoke in protest since Monday this week, according to Dutch news agency ANP.
Less than a quarter of the Dutch population of 16.4 million are smokers.