Athens has allowed hydrocarbon exploration and exploitation rights off the island of Crete and in the Ionian Sea in recent years to the dismay of local activists.
Conservationists say the seismic research can cause hearing damage and stress to cetaceans.
On Tuesday, 15 environmental groups urged a halt to the research after three Cuvier's beaked whales washed up alive at the island of Corfu since Sunday, according to WWF's Greece chapter.
"Seismic research conducted in the area must stop immediately" until it is clear what caused the whales to wash up, said the letter, posted on WWF's website.
The letter's signatories, which included Greenpeace and Medasset, was addressed to Greek Prime Minister Kyriakos Mitsotakis and environment officials.
According to marine wildlife experts, Cuvier's beaked whales live at depths of over 1,000 metres (3,280 feet) and are acutely sensitive to noise pollution from human activity.
The groups said a survey ship has been conducting research in the Ionian Sea since February 10.
The area has also seen additional traffic from rescue vessels after an Italian-flagged ferry caught fire northwest of Corfu on February 18.
An adolescent member of the dolphin-like species also beached itself on the coast of Athens last month. It died a few days later.
Greek government officials did not immediately reply to the letter.
AFP has requested a comment from the environment ministry.
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