Local mayor Bessaou Ismak Ado Crophe on the resort island of Sainte Marie told AFP both bodies showed signs of head trauma, with officials suspecting murder.
"They spent the evening in a nightclub and were found on the beach nearby," he said.
"I saw the bodies. Both had injuries to the head."
The victims, a man and a woman in their twenties, were volunteers at Cetamada, a local environmental non-profit organisation working to protect ocean mammals.
An investigation had been launched.
"The government strongly condemns this act and will ensure that the investigation will be transparent," he said.
Cetamada vice-president Jean-Jacques Ravello, who is also France's honorary consul to Sainte Marie island, called the incident "barbaric".
"I do not want to minimise this barbaric act, but we've been bringing dozens of volunteers here for 15 years and we've never had a problem this big," he told AFP.
He said the volunteers had gathered together following the incident and were "shocked psychologically".
A year later, two Europeans were attacked and killed by a mob on the northwest island of Nosy Be, suspected of involvement in the death of an eight-year-old local boy.
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