The Shanti Nagar police, under whose jurisdiction the incident took place, said the mishap occurred around 11 AM.
The deceased, who were trapped under the debris as the toilet caved in, were identified as Mahavir Kesarwani (55) and Mazhar Mohamad Alam (22), police said.
The three injured were admitted to a local hospital and were undergoing treatment.
Police have registered a case of negligence against the contractors, responsible for alleged sub-standard construction.