The Environment and Resources Authority insisted the black liquid being discharged at sea behind Fort Ricasoli was “not within its remit”.
Footage of liquid shot on August 4 by a resident shows hundreds of white maggots in the polluted liquid on the rocks.
Witnesses also said the liquid discharged just metres away from a public bay emitted a foul smell.
Liane Gatt, who produced the footage, asked: "This is a public place. Families come here. Children come here or in the surrounding areas to swim. How can this be allowed to happen?"
The Environment Ministry was asked what action would be taken to clean up the area and what preventive measures had been taken at the site.
“The case was investigated by ERA and it was found that the water pollution in question resulted from fly-tipping in the area.
The water pollution in question resulted from fly-tipping in the area
“The latter illegal activity does not fall within this authority's remit,” an Environment Ministry spokesman replied.
Sources said the issue fell within the local council’s remit, however, efforts to contact the local council were futile by time of writing.
Wirt il-Kalkara general secretary Duncan Brincat said long-standing environmental and health issues in the area have left residents “sensitive and wounded”.
Multiple individuals had submitted police reports, he said, with many lamenting the dark liquid was evidence of the carelessness with which environmental issues were being handled.
“We absolutely condemn this,” Mr Brincat said, adding that there was “clearly something illegal going on”.
Reports of black effluent being discharged in the area date as far back as 2015.
Waste Oils Limited, the company reportedly responsible for the effluent, had said it could not provide a rational explanation for what had happened. The company had said water may have turned black inside some equipment that had not been used for some time and was now leaking out.
The company had also told Times of Malta any equipment used in the treatment of water would be flushed clean before any intended suspension of use “to ensure that this possibility does not recur”.
Last year, a video with black liquid streaming into the sea at Ricasoli had also gone viral, with ERA again insisting the effluent came from a tank cleaning facility operated by Waste Oils Limited.