Roby Gasser told the Nordwestschweiz publication that the deaths of the marine mammals in November 2011 were not accidental.
Conflicting reports followed the death of the dolphins, called Shadow and Chelmers, which coincided with a rave party for thousands of clubbers that was held on land rented from Conny-Land.
A toxicology report leaked in May indicated the dolphins were likely killed by a heroin substitute.
They died within five days of each other after a long period.
Gasser said that rather than an incident connected to the party, he believes the dolphins were deliberately killed by the former employees, who worked as animal keepers.
“These people have changed camp,” he told Nordwestschweiz.
“They now work for German animal protection organizations.”
Gasser believes they are the only ones who would have known what food the dolphins liked.
He said the dolphins that died were male and were particularly targeted because of their genders.
“The Swiss law for the protection of animals no longer allows us to import this kind of species,” Gasser said.
“And the females cannot reproduce without males.”
Prosecutors were initially considering negligence charges in the dolphin deaths because they believed antibiotics given by zoo vets were to blame.
But later tests by a Saint Gallen forensic institute showed traces of Buprenorphin, a heroin substitute, in the mammals’ urine.
Such an opiate may have caused the dolphins breathing difficulties.
Justice authorities in Kreuzlingen are declining to comment on Gasser’s views.
Conny-Land continues to offer a dolphin attraction using an artificial lagoon consisting of an 81-metre long basin, 35 metres wide and six metres deep, which the operator says cost more than 1.5 million francs.