Daniel Agger played for the various Denmark youth teams before making his debut for the senior team in 2005. The defender featured for the u-20 team and the u-21 team before playing his first game for the senior team.

Agger scored once in ten games for the Denmark u-20 teambetween 2003 and 2004. He also scored three times in ten matches for the Denmark u-21 team between 2004 and 2006. His senior team debut came in a friendly match against Finland on June 2, 2005. The centre back played the whole game which ended in a 1-0 victory for the Danes. He was then benched for the next senior national team game. His second cap came against England on August 17, 2005. Daniel Agger partnered Per Nielsen at the heart of the Danish defenceduring a friendly game which ended in a 4-1 win for his team.

Daniel Agger scored his first senior national team goal during the 6-1 win over Georgia at home in a qualifier for the 2006 FIFA World Cup tournament in Germany. He was unable to help his country reach the tournament on German soil. The defender was part of the Denmark squad to the 2006 UEFA u-21 European Championship.

Agger was on target for the Denmark senior team in a 3-3 draw with Scandinavian rivals Sweden on June 2, 2007. The game was a qualifier ahead of the Euro 2008 tournament in Austria and Switzerland. The game was stopped in the final minute due to crowd trouble and the points awarded to Sweden. He scored once in eight qualifying games as Denmark reached the 2010 FIFA World Cup tournament on South African soil. The lone goal came during the 3-0 win over Malta at home. Daniel Agger scored an own goal against the Netherlands in the first group game for Denmark at the World Cup tournament in South Africa. He was involved in the other two group games as the Danes exited the tournament at the group stage.