The Japanese fleet, which had its own refuelling tanker, had to suspend the hunt last month after confrontations with activists from both groups.
On January 15 two activists from the Sea Shepherd Conservation Society boarded a Japanese harpoon ship to deliver a protest letter, setting off a two-day standoff.
Both Greenpeace and the more militant Sea Shepherd group sent ships to trail the Japanese whaling fleet, hoping to disrupt the whale hunt and stop more whales from being killed.
An Australian media report last Friday said a coastguard vessel had seen Japanese harpoonists kill five whales in one day after the protesters left the area.
On January 15, an Australian court, in a symbolic ruling, ordered an end to Japanese whaling in its Antarctic waters.
Japan has to defend its whale-hunting programme saying the plan to slaughter about 1,000 whales this year is legitimate scientific research.
But critics dismiss the programme as a disguise for commercial whaling which has been banned by the International Whaling Commission since 1986.
A loophole in the ban however allows limited whaling for scientific research.
Last year, Japan's southern ocean whaling season ended early after its factory ship, Nishin Maru, was crippled by fire while hunting in the Ross Sea area killing one crew member.