The shooting took place in the Södra Sofielund neighbourhood of the city, reports news agency TT.
A police patrol arriving at the scene found the two men injured by the shots after witnesses raised the alarm to the incident at around 15:30 on Friday.
“It is relatively unusual that shots are fired during a robbery,” Calle Persson of Malmö Police told TT.
Either three or four men stormed into the shop and threatened the two men who were shot, according to police.
“The robbers shouted ‘where is the money, where is the money’ and then he shot me, first in one foot and then in the other,” the shop’s owner told the Kvällsposten newspaper.
According to local media reports, several people were seen fleeing the scene, but police have not yet determined how many fired shots or how many shots were fired.
The area was cordoned off for police investigation on Friday evening.
Police have not currently detained any suspects in connection with the incident. The extent of the victims’ injuries is also unclear, but both were able to speak as they were taken to hospital by ambulance.
Persson, spokesperson with the police Region Syd (South) department, told TT that witness statements and other material would now be examined.
“We have taken in material from surveillance cameras,” he said.