The Lost Dogs' Home said between July and December 2021 the amount of "pocket pets" arriving at their North Melbourne and Cranbourne shelters rose from 20 to 53.
Shelter supervisor Allie Small said there were several factors behind the increase, including the rising cost of buying dogs from breeders during the pandemic and demand outstripping supply for animals at shelters.
"The difficulty people had getting a pet during this period has led them to look at different alternatives," she said.
"Pocket pets may be small, but they are as deserving of our love as their larger counterparts such as dogs and cats.
"It is heartbreaking watching so many of them, often not microchipped, being abandoned in such alarming numbers.''
She said another reason was people often perceived animals like rabbits, guinea pigs and ferrets to be low-maintenance.
This often led to people surrendering or rehoming these pets as they could not appropriately care for them.
While they may not cost as much to purchase and set up at home, ongoing maintenance of rabbits and guinea pigs, including feeding and medical care, is often more specialised than dogs or cats and can become expensive over time.
The shelter is working with its rescue and corporate partners to rehome the pets.