The measures aim to "prevent important damages and protect public health and safety", the environment ministry said in a statement.
A government-appointed commission of scientists backed the move, saying that it did not "endanger the conservation of these two species".
The decision to let the authorities carry out the killings also "prevents trophy hunting", according to the experts.
But the World Wide Fund for Nature (WWF) strongly denounced the measure and blamed the issue on deforestation.
Last October, a similar outcry forced the environment ministry to retract quotas allowing hunters to kill 552 bears, 657 wolves and 482 lynxes.
Romania's vast areas of virgin forest are home to around 6,000 brown bears -- some 60 percent of Europe's population -- which mostly roam the Carpathian Mountains.
In recent months, an increasing number have entered towns and villages looking for food.
In July, two shepherds were seriously injured in a bear attack in the Carpathian region.
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