The Sea Shepherd Conservation Society said in a news release Saturday that it deployed one of the drones to intercept the Japanese factory ship Nisshin Maru about 800 kilometres off Western Australia's southwest coast.
Canadian Captain Paul Watson who is onboard the ship, Steve Irwin, said the drones also allow the conservationists to keep track of the whalers when they try to escape.
"What they do is they put these harpoon vessels on our tail and they relay our position to them (the Nisshin Maru) and it keeps the Nisshin Maru away," said Watson during a telephone interview. "So with the drone we're able to, you know, keep abreast of where the Nisshin Maru is."
He said as of Christmas Day, two Japanese harpoon vessels were still trailing his ship, the Steve Irwin.
Watson said one of the drones was donated by two companies from New Jersey.
According to media reports, the Japanese whaling expedition left earlier this month and plans to take 900 whales.
Watson said the Japanese are hoping to cull 935 minke whales, 50 fin whales and 50 humpback whales, but haven't killed any animals yet.
Watson said three Sea Shepherd ships, the Steve Irwin, the Bob Barker and the Brigitte Bardot, which are crewed by 88 people from 25 different countries, are monitoring the Japanese fleet.
He said the Sea Shepherd ships left Western Australian and Tasmanian ports about one week ago and will be monitoring the fleet until March, when the whaling season is expected to wrap up.
Conflict between the conservationists and Japanese is nothing new. An at-sea collision between whalers and conservationists last January sunk one Sea Shepherd boat.
The Sea Shepherd Conservation Society was formed in 1977 and has had a controversial history.
The group sends vessels to confront the Japanese fleet each year, trying to block them from firing harpoons at whales.
The group's tactics have drawn praise from supporters and vehement attacks from critics.
Watson made a lot of enemies in Newfoundland and the Maritimes with his opposition to the annual seal hunt.
In 2008, two crew members of a Sea Shepherd Conservation Society ship, the Farley Mowat, were charged and convicted of interfering with the hunt.