From September 2004 he also held the position of Acting Minister of Internal Security after Tzachi Hanegbi resigned in the face of corruption allegations.

This ministerial post was also made permanent in November, and Ezra oversaw the evacuation of the Amona settlement in February 2006.

In November 2005 he was attacked during a rally in Sderot against Israel's unilateral disengagement plan over his support for it.

When Sharon founded Kadima in late 2005, Ezra joined him, picking up the Environment Ministry portfolio from Labor's Shalom Simhon.

In April 2007 he opposed plans to build a solar energy plant near Dimona to avoid harm to a nature reserve.