This is the third time Ms Frederiksen postpones the events which was originally set to take place this summer. The meeting, set to take place on July 17 and 18 will observe plans for a coronavirus recovery fund.
It will be the first summit officials will attend personally since the coronavirus pandemic forced countries to go into lockdown.
Ms Frederiksen and her partner, Bo Tengberg, would have gotten married on July 18.
In a statement published on the prime minister’s Facebook account she said she had to “protect Denmark’s interests”.
Denmark has disputed the fund over a proposal to extend grants to nations that were highly damaged by the pandemic.
Denmark as well as Sweden, Austria and the Netherlands say the suggested £676bn (€750bn) for the fund is too much money and have reiterated that any funds granted must eventually be paid back.
The date of the EU meeting, which will take place in Brussels, was revealed in recent days.
In a Facebook post, Ms Frederiksen wrote: “I am so looking forward to marrying this amazing man.
“But obviously it shouldn’t be easy, and now the Council meeting in Brussels has been convened precisely on Saturday in July, when we had planned a wedding.
READ MORE: Christianity news: Trump has election BOOST over Biden from christians
The center-left Socialist Democratic party leader became Denmark’s youngest prime minister last year at the age of 41.
Denmark has registered 12,836 coronavirus infections and 603 deaths, according to data from Johns Hopkins University.
It was one of the first Western nations to start lifting lockdown measures in April.
Last August, US President Donald Trump accused Ms Frederiksen of making “nasty” and “inappropriate” remarks, after she branded his alleged idea to purchase Greenland as “absurd.”
Speaking to journalists on the White House lawn last year, Trump lashed out at Ms Frederiksen’s comments.