Daniel Agger started his international career for Denmark in the colours of the u-20 team as he scored once in ten appearances between 2003 and 2004. He then scored three goals in ten games for the Denmark u-21 team over a two-year period. Daniel Agger played for the u-21 team from 2004 to 2006.He had already made his senior team debut by the time he finished his last game for the u-21 team.

Agger made his senior team debut for Denmark during the 1-0 away win over Finland in a friendly game played in Tampere on June 2, 2005. The central defender played the whole game as he helped his country keep a clean sheet. Despite the clean sheet, Daniel Agger returned to the Denmark bench for the next game before he returned to the Denmark starting XI as the centre back partner of Per Nielsen during the 4-1 friendly win over England on August 17, 2005.

Daniel Agger found the back of the net for the first time when Denmark beat Georgia in a qualifier ahead of the 2006 FIFA World Cup tournament in Germany. The defender scored one of the goals in a 6-1 home win over Georgia on September 7, 2005, but the victory counted for nothing in the end after the Danes failed to qualify for the tournament.

Agger scored his second goal for the Denmark senior team during the 3-3 home draw with Scandinavian rivals Sweden during the qualifying campaign for the Euro 2008 tournament. The Sweden game was abandoned in the last game due to crowd trouble with the three points awarded to the Swedes.

Daniel Agger played eight times with a return of one goal during the qualifying campaign for the 2010 FIFA World Cup tournament in South Africa. His lone goal came during the 3-0 home win over Malta. Agger qualified for his debut major tournament with his country at the 2010 FIFA World Cup tournament on South African soil. He played in all three group games as Denmark exited the World Cup tournament in South Africa at the group stage. He also played for Denmark at Euro 2012. Agger finished his senior team career with 11 goals in 75 games.