The incident happened after a flea killer was administered incorrectly to the Alsatian bomb-sniffers at the Defence Animal Centre in Melton Mowbray in Leicestershire, The Sun reported.
The ministry said that 18 dogs became ill last month after a flea killer that should have been put on their backs, was given to them orally.
While 15 of the dogs made a full recovery, three died.
The dogs perished in "horrific circumstances" after the deadly chemical was put in their grub, the paper said.