The ministry will extend the measure for a further six months effective from November 11th, when the current border control expires.
The Danish ministry cited a “serious terror threat” against Denmark as the primary reason for the continuation.
A number of rules must be complied with in order for Schengen countries to implement temporary border control.
When it extended border control one year ago, Denmark changed its justification for the measure from the high flow of migrants to the country - the original reasoning from 2015 - to also citing a stated terror threat.
Terror is now the primary reason for continuation of border control, according to Friday's ministry statement.
"The government has succeeded in bringing arrival and asylum figures to a low level, which I am pleased about. Nevertheless, there remains a serious terror threat against Denmark and considerable pressure on Europe's outer borders. The government therefore believes border control is necessary to protect Denmark's security," immigration minister Inger Støjberg said in the statement.
The government has informed the European Commission and other Schengen member states of the decision, the ministry confirmed.
The temporary border controls were first introduced on January 4th, 2016 and have been renewed on several occasions by the government.
“We live in the real world and in the real world, there is a serious terror threat against Denmark,” Støjberg told news agency Ritzau on Friday.
Denmark has been in close consultation with other Schengen countries that currently have temporary border controls – Germany, Austria, Norway and Sweden – over the decision, Støjberg also said.
“We are keeping close contact with regard to border control. I know that the other countries will also be making announcements soon,” she said.
Austria announced Thursday that checks on its borders with Hungary and Slovenia would be extended by six months, and Støjberg expects similar extensions from the remaining three countries.
The minister did not comment on for how long border controls might continue to be extended.