They succeeded in excluding Iceland which wants to join the IWC while keeping open the option of a return to commercial whaling.
Japan has been leading the drive for a resumption of commercial whaling, banned 15 years ago, at the meeting held in the port of Shimonoseki in western Japan, home to the country's whaling fleet.
The vote over Iceland's membership was seen as a key test of sentiment as the conference got under way.
Pro-whaling countries tried to overturn last year's ruling that Iceland could not join until it agreed to accept the IWC's moratorium on commercial whaling.
They were defeated by 25 votes to 20 despite their optimism that this time they could muster the necessary majority.
Iceland has had non-voting observer status since its delegates walked out of an IWC meeting 10 years ago to protest against the commission's anti-whaling stance.
Its return to full membership could have given the pro-whaling nations a majority.
The UK Fisheries Minister, Elliot Morley, said the result was better than expected and a very good sign, but he cautioned that anti-whaling countries could face tougher resistance on other issues.
There is a suspicion some delegates may have been confused by the hours of procedural wrangling before the vote was taken and by its wording.
Stormy days ahead
In the coming days, Japan will seek support for an expansion of its research whaling programme which currently takes about 500 minke whales a year.
It will also seek to block proposals for new whale sanctuaries in the South Pacific and South Atlantic.
Japan says some species of whales are so abundant they are threatening fish stocks.
The United States has described the claim as false and an attempt to make the whale a scapegoat for over-fishing.
Six countries have joined the organisation in recent weeks and four are thought to back Japan's position.
Environmental groups have accused Japan of buying the votes of new members with development aid.