The decision to keep the measures in place was expected after the EU Commission approved an appeal from five Schengen countries to once again extend the border controls by three months.
Denmark's controls, which have been in place since January 4th, 2016, were due to expire on February 12th but will now remain in effect through May.
The Danish extension comes despite the nation's asylum numbers falling drastically in 2016. Roughly 21,000 asylum seekers entered Denmark in 2015 but last year there were just 6,072.
“It's true that we are very, very low when it comes to the number of asylum seekers at the moment. As it looks now, we are at the lowest level in five years but things can very quickly change,” she told news agency Ritzau.
Støjberg said the Danish government would continue to push the EU for permission to extend its border controls “until Europe's order borders are under control”.
“Denmark will have border controls for as long as it is necessary to have border control,” she said.
The other Schengen nations to request permission to extend border control measures are Sweden, Norway, Austria and Germany.