"We have had many examples over the last number of years where we felt that the state aid rules were not generous enough in helping member states deal with crisis in their country from time to time," he told AFP.
The new ceiling comes into force in March, he said.
However, limits on the total amount member states can pay out to their agriculture sector will remain in place.
Hogan said the new measure "struck a balance" between the need for more capacity to help farmers in need, and any danger of distorting competition with excessive subsidies.
"We would be blamed for not having a level playing field," he said.