Sea Shepherd Conservation Society spokesman Paul Watson said the unmanned long-range drone, launched from the anti-whaling ship the Steve Irwin, had located the Japanese fleet and relayed the coordinates back to the activists.
Watson said Sea Shepherd, a militant activist group which regularly shadows and harasses the Japanese whalers, had caught up with the fleet at 37 degrees south, 1,000 miles (1,600 kilometres) above Antarctic waters.
No whales had been killed so far, he added.
"This is going to be a long hard pursuit from here to the coast of Antarctica," said Watson.
"But thanks to these drones, we now have an advantage we have never had before -- eyes in the sky."
Three Japanese security vessels were tailing the Steve Irwin to prevent it from following the Nisshin Maru factory ship, Watson said.
But he said the activists had established the upper hand with their two drones, donated by Moran Office of Maritime and Port Security (MOMPS), a private US firm.
Fitted with cameras and detection equipment, the drones have previously been used to combat bluefin tuna poaching off Libya.
Unmanned aircraft are most notably used by US forces in Pakistan and Afghanistan.
The Sea Shepherd drones were developed by New Jersey-based MOMPS, which is described as working to enforce international maritime and fisheries rules and "helping to prevent acts of terrorism and piracy worldwide".
Watson said: "We can cover hundreds of miles with these drones and they have proven to be valuable assets for this campaign."
While the Steve Irwin was being tailed by the harpooners' security detail he said Sea Shepherd's other vessels the Bob Barker and Brigitte Bardot -- which can travel faster than the whalers -- were free to chase the Japanese south.
Commercial whaling is banned under an international treaty but Japan has since 1987 used a loophole to carry out "lethal research" in the name of science -- a practice condemned by environmentalists and anti-whaling nations.
Australia, New Zealand, the United States and the Netherlands issued a joint statement earlier this month expressing their "disappointment" at the annual hunt and warning against violent encounters.
Confrontations with the increasingly sophisticated Sea Shepherd group have escalated in recent years, with one clash sinking an activist powerboat and a protester arrested for boarding a Japanese ship.
Sea Shepherd harassment saw the Japanese cut their hunt short last season, and they are now suing the activists in Washington seeking an injunction against what they say is a "life-threatening" campaign.
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Japan's coastguard has deployed an unspecified number of vessels to protect the whaling ships, and Tokyo has confirmed it will use some of the public funds earmarked for tsunami reconstruction to boost security for the hunt.