The two dogs – PC Ebony and PD Cuzo – were uninjured in the incident, Lancashire Police said.
Officers had been responding to reports of a party taking place in Whitworth, Rossendale, around 2.25am on Monday morning.
A small gathering was found, a spokeswoman for the force said, and three men were spoken to and left the house willingly.
But, when one of the officers returned to his vehicle, which had been parked in a nearby street, he found it the rear window had been smashed.
“Two police dogs – PD Ebony and PD Cuzo – were inside the van at the time, but thankfully they weren’t harmed,” the spokeswoman said.
Posting on Twitter, Lancashire Police Dog Unit said the incident was “not acceptable”.
It said: “Tonight whilst dealing with a report of a house party, in Whitworth. One of our vehicles carrying two police dogs inside was bricked, showering the dogs with glass!
“Thankfully both dogs are uninjured however it took a response vehicle off the road.”
The spokeswoman said no arrests have been made but enquiries are “very much ongoing”.