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The earthquake damaged a few large paper mills up in the Miyagi prefecture belonging to Nihon Paper Group and Mitsubishi Paper Mills - both of these companies make up 20% of the market share for paper.

Another problem is that the earthquake caused liquefaction of land in Tokyo around the bay area - many buildings started to sink and many roads were destroyed meaning that warehouses used for paper distribution are unusable.

Ink is also in dangerously low supplies too after ink factories were damaged in the quake. The rolling blackouts, shortage of gasoline are also factors affecting the ability for the factories to get back up on their feet again.
The raw ingredients needed to make offset ink, newspaper ink, gravure ink are in particularly low supply.

The shortage of ink and paper is going to have an impact on the publishing industry which has been called on to take special measures to deal with the current situation.
Some industry writers have mentioned that some publications will have to either cut down on the amount of pages in their publications or change the frequency that they go on sale - from once a week to every two weeks for example.
We will also most likely start to see a drop in the amount of colors used in publications to product packaging.

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