The tuna farms have been told to stop feeding fish in their pens with immediate effect, until mitigation measures are in place to stop slime from escaping.
The Environment Ministry said on Thursday that tests - including on-site inspections - were carried out by the Fisheries Department and by the Environment and Resources Authority had left no doubt as to the origin of the slime.
The ministry said that the operators were clearly not abiding by the terms of their permit and that the department and the authority were instructed to take action against them to the full extent of the law.
The federation, which has a number of operators as its members, has committed to work with the government to ensure that this is done.
Sea slime appeared along the coast in Marsascala, Sliema and other areas on Tuesday, prompting fears of a repeat of problems that plagued beaches two years ago.
In 2016, the widespread incidence of a similar, oily slime led to public outrage and the eventual suspension of permits for tuna farms around the island after they were identified as the source.
The farms have since been given new permits to operate in designated acquaculture zones around six kilometres offshore, coupled with more stringent environmental measures to prevent a recurrence.
However, Tuesday's slime drew particular concern, as it coincided with the start of the tuna feeding season. Two years ago, the use of a new fish feed with a higher fat content was identified as the main cause.
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