The migration has picked up in the last six months amid increasing Sunni-Shia violence and is further deepening the country's sectarian divisions, Abdul-Samad Sultan said on Tuesday.
Some 890,000 other Iraqis have also moved to Jordan, Iran and Syria in the last three years, he said.
The people who have moved within Iraq have gone to areas where their own community dominates.
In particular, Shias have left Sunni-majority or mixed areas and the Sunnis have moved in.
"We had hoped that the situation would help us after Saddam's fall. But unfortunately, the plans of the Saddamists and the terrorists have shaken the new Iraq," Sultan said.
"This is the goal of the terrorists, to create [separate] Shia and Sunni pockets and change the demographics of Iraq".
Large numbers of Arabs have also fled to the relatively peaceful Kurdish areas of northern Iraq.
Statistics released by the ministry showed that 51,000 families had fled for other areas of Iraq. The ministry assumes there is an average of six people in family which means there are 306,000 displaced.
Sultan said at least half of them fled their homes after the bombing of a Shia shrine in the city of Samarra in February which sparked a series of retaliatory against Sunnis.