While Asia and west and central Africa bore the brunt, 1.3 million were displaced in rich countries, with Hurricane Sandy in the United States accounting for 900,000 alone, the Geneva-based IMDC said.
Internally displaced is a label given to individuals who remain in their homeland, to distinguish them from those who cross borders and are counted as refugees.
The hardest-hit countries in 2012 were India and Nigeria.
Flooding in both countries forced 6.9 million and 6.1 million people, respectively, to flee.
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But in 2012, Africa reached its high-ever number with 8.2 million people newly displaced. The figure was quadruple that seen in any of the previous four years.
Natural disasters compound the impact of other crises, the IMDC underlined.
"In countries already facing the effects of conflict and food insecurity such as in Nigeria, Pakistan, and South Sudan, we observe a common theme," spokeswoman Clare Spurrell said in a statement.
"Here, vulnerability to disaster triggered by floods is frequently further compounded by hunger, poverty and violence, resulting in a 'perfect storm' of risk factors that lead to displacement," she added.
While Hurricane Sandy spotlighted the impact of extreme weather on rich nations such as the United States, the IMDC noted that poor nations bore the biggest burden by far.
"In the US following Hurricane Sandy, most of those displaced were able to find refuge in adequate temporary shelter while displaced from their own homes," said Spurrell.
"Compare this to communities in Haiti, where hundreds of thousands are still living in makeshift tents over three years after the 2010 earthquake mega-disaster, and you see a very different picture," she added.