"Yesterday evening the French Ministry of Environment asked us to temporarily stop sending bears to France," the Environment Ministry said in a statement, without giving further details.
Slovenia and France agreed in 2005 to send five brown bears to France's Pyrenees region this year to help boost the bear population.
Slovenia transported two female bears to France in late April. The remaining bears were due to be transferred by the end of August but farmers in the Pyrenees protested against the move which they say would threaten local people and livestock.
The Slovenian news agency STA said the decision to stop further transfers followed the discovery of 12 containers in which bear food was mixed with pieces of glass in the area where one of the bears was moved to.
With around 550 bears in the wild, Slovenia has one of the largest bear populations in Europe. Dense woods, which are their ideal habitat, cover more than half of the small Alpine country.