The case was part of a kit for geologists to measure the density and humidity of the earth and contained "two sources of low-level radioactivity," said the agency, the CSN.
It disappeared on Tuesday from a vehicule in the town of Mostoles, outside Madrid, and was probably stolen, it said in a statement.
"The material that was removed presents no radiological risk if it remains closed and intact, since the radioactive sources are inside and protected in capsules," it said.
But the material could "pose risks if it is opened or the equipment destroyed," the CSN warned.
The agency released a detailed description of the equipment and an appeal to the public to be careful.