Local newspaper Sydsvenskan spotted dozens of the dead animals floating in the waters of both Kungsparken and the adjoining Castle Garden (Slottsträdgården) last weekend.
The most likely cause is believed to be overflow from urban drains following heavy rain.
“In all likelihood it came from surface water pipes,” Peter Nilsson, an official at Malmö’s Streets and Highways Agency told Sydsvsenskan.
“With heavy rain the water flushes out rats that were lying dead in the pipes. Even live rats could have been swept away and drowned,” he added.
Rats have been flushed into the city’s waterways before, but according to Nilsson this is the first time that the phenomenon has occurred in a number of years.
Over the course of Monday the local municipality removed 141 of the dead rats from the canal, giving summer workers like Sanne Svensson an unusual day at the office.
“To begin with it was really disgusting. The rats were big and bloated, and also smelled. But you quickly got into it and got used to it,” she told news agency TT.
The rats were picked up with tools normally used to lift litter, then placed in plastic bags which will be incinerated. The municipality believes all have now been removed from the water.
Most of the rats were found around the canal's pumping station, where they were washed out of the drainage system by heavy rain, though some had floated further out.
Malmö was drenched in harsh rainfall last weekend, with storms marking the end of Midsummer celebrations in the southern Swedish city.