They will assist in the debris removal in the valley of the Savinja River.
Record high amounts of rain in a day fell in Slovenia last Friday, and the extreme weather and flooding have taken six lives and caused huge material damage.
Over the weekend, a Croatian Air Force helicopter was engaged in efforts in Lendava to build concrete flood barriers.
On Monday, the Croatian government held a conference call to approve the additional assistance for the flood-affected areas in the neighbouring country and to give a greenlight for army troops to cross the border with Slovenia to help locals in clean-up in the wake of the worst flooding recorded so far in Slovenia.
The ministry also offered condolences over the casualties.