The Japanese government-sponsored Institute of Cetacean Research said in a statement on Wednesday that a Sea Shepherd vessel had come dangerously close to a Japanese craft and tried to blind its crew with lasers.
The Ady Gil, which has joined Sea Shepherd ship the Steve Irwin as part of the annual anti-whaling campaign in Antarctic waters, had also "fired ball-like projectiles with a projectile-launching device" during an attack lasting three-and-a-half hours, the centre said.
Sea Shepherd accused the Japanese of using crowd-control sound technology known as a Long Range Acoustic Devices, or LRADs, as well as water cannon, against the Ady Gil crew.
The activists said they responded with lasers to get the Japanese to back off to a safe distance.
The Japanese accuse both Sea Shepherd ships of trailing ropes in failed bids to entangle the whaler's rudder and propellor.
They also accused the Steve Irwin crew of hurling bottles of butyric acid - a rancid liquid that occurs in spoiled butter - during a two-hour conflict on Tuesday.
Steve Irwin captain Paul Watson said the "acid attack" was stink bombs the crew threw at the Japanese in a bid to "annoy them".
Capt Watson said earlier on Wednesday that his crew had been unable to shake off the Japanese security vessel Shonan Maru No 2, which has been chasing and harassing his ship to keep it off the trail of the Japanese whaling fleet.
He said the Ady Gil was called in to create a diversion and allow his crew to pursue the whalers.
The Ady Gil, a 24-metre trimaran "stealth boat" painted with radar deflective paint, had circled the Shonan Maru in a bid to slow it down, he said.
"At first it looked good, and the Steve Irwin was able to put 12 miles between the Shonan Maru No 2 and itself," Capt Watson said.
"But despite being harassed by the Ady Gil for two hours, the Japanese slowly worked their way back to a six-mile distance.
"To accomplish this they had to increase their speed to over 20 knots, a speed at which, unfortunately, the Steve Irwin cannot outrun."
He said the Ady Gil was carrying five crew members - four New Zealanders and one Dutch citizen.
Australian Greens leader Bob Brown has called on the federal government to send surveillance planes or boats to record the dispute.
"This is a whaling war with Kevin Rudd missing from action," Senator Brown said.
"Japan has two naval vessels involved. Rudd should at least send surveillance planes or vessels."
Senator Brown says he is revolted that Japan's fleet was allowed to refuel in Australia en route to killing whales.