"(We) expect that the quota will ensure favourable conditions for the (brown bear) population," the ministry said in a statement on Friday.
The quota was based on an estimate that there are 500 to 700 brown bears in Slovenia and on the government view that the number of bears would become excessive unless kept in check.
A total of 121 brown bears died in Slovenia last year, mainly as a result of hunting and traffic accidents.
The World Wild Fund (WWF), a top global conservation organisation, said it believed the quota was too high and estimated there are only 500 bears in Slovenia.
"The WWF is very concerned that this quota is too high and will affect the whole population of brown bears, including countries like Austria, Croatia, Bosnia and Herzegovina, Serbia, etc.," Gerald Dick of WWF Global Species Programme told Reuters.
"There is no clear evidence provided about the population size, therefore the quota lacks scientific grounds and is not sustainable," he said.
Slovenia has one of the largest bear populations in Europe and last year exported five bears to the French Pyrenees to increase the number there, despite protests by French farmers.
Dense woods, the bears' ideal habitat, cover more than half of Slovenia, a small Alpine country with two million people.