A petition to the assembly wants it to be mandatory to scan microchips of all pets, dead or alive.
RSPCA Cymru said it backed mandatory identification of pets killed on highways so owners know what happened.
One of six councils which does not scan said it was reviewing its policy, but two others have no plans to change.
The petition says: "The microchip system can only be fully effective if animals that have been microchipped are scanned and this is vital for the owners who have to endure the mental torment of never knowing and continuing searches for weeks/months when a family pet goes missing."
The petition has more than 160 signatures - at present, petitions need 10 names before they are considered, but proposals are being discussed to increase that to 50.
Cats Protection wants it to be compulsory for people microchip their animals - a law covering dogs came into effect in April 2016.
When the Welsh Government developed microchipping regulations, a survey of councils found most routinely scanned dead dogs found on the roads and informed owners when possible, so compulsory scanning was not included.
The petitions said only Gwynedd, Anglesey, Cardiff, Newport, Blaenau Gwent and Neath Port Talbot councils do not routinely scan animals.
The rest do "when they deem the animal in a state to do so" but the petition calls for this to cover all domestic animals, regardless of their condition, and their owners notified.
"Whilst it is considered the unfortunate upset or distress the street clean may endure when scanning animals found in a bad way, the fact is they will handle these animals regardless of our proposed policy," it said.
Cardiff council said dead dogs were scanned and taken to the pound, but not cats - which the authority has been petitioned about separately.
Neath Port Talbot said it was reviewing the situation in light of several requests, Blaenau Gwent said it had no plans to scan, as did Anglesey - stating it was not part of its street cleaning contract with a private firm.
RSPCA Cymru said it was "deeply sad" owners of many animals killed on the roads were "unable to locate them or learn their fate".
The charity wants to see mandatory identification of pets and their owners notified in when they are killed on highways.
Animal lovers hope to make it mandatory for pets found by council workers to be checked for microchips so they can be returned to their owners.