The showdown occurred at the International Whaling Commission's annual meeting in the Caribbean state of Kitts and Nevis.
"So far we have managed to dodge the harpoon, but let's see how things go for the rest of the week," said Dr Joth Singh of the International Fund for Animal Welfare.
Conservationists were celebrating after Japan failed to secure enough votes on the International Whaling Commission (IWC) to institute secret balloting and bar members from discussing protection for porpoises.
The proposal to introduce secret balloting failed by 33 votes to 30 while the motion on porpoises, which some conservation groups consider endangered, was also narrowly defeated by 32 votes to 30 with one abstention.
Both items were considered key to Japan's attempt to establish a pro-whaling majority on the commission for the first time since a moratorium on commercial whaling came into force two decades ago.
The moratorium on commercial whaling is not under immediate threat as it needs a 75 percent majority in the IWC to be overturned.
However whaling opponents fear a simple voting majority would enable Japan to chip away at the moratorium by turning the IWC into a "whaling club."
Mike Townsley, a Greenpeace spokesman, said Japan's efforts appear to have been thwarted. "They stumbled on the first vote and fell on the second and it is clear Japan has failed to take over the IWC," he said.
Australia: cautious optimism
Ian Campbell, environment minister of anti-whaling Australia, was more cautious. "They have had a couple of votes go against them," he said, but Japan could still manage to muster enough votes for a simple majority on pending items.
Togo, which missed two votes in the morning, showed up late but was expected to vote with Japan in future balloting, sources on both sides of the debate told AFP.
Dr Singh said conservationists would now turn their efforts to limiting the number of whales killed in ongoing hunts by Japan, Iceland and Norway.
Japan and Iceland conduct "scientific" whaling while Norway disregards the moratorium entirely.
Japan has not given up
Japanese sources said they had not given up hope of establishing a majority for pro-whaling nations on other issues at the five-day conference.
Earlier, Japan warned it could pull out of the organization if there was no progress towards its goals "within a few years."
Green campaigners accuse Japan of bribing small, developing states like Cambodia or Mongolia which have little interest in whaling, to join the commission with foreign aid.
Japan argues the moratorium on commercial whaling has been so successful that whaling of certain species can now be carried out without harming whale stocks.
Tokyo denies claims it bribes small states with aid, pointing out that it also supports nations which oppose whaling, such as India and Argentina.