While the resolution is not binding and will not overturn the moratorium, it is a significant victory for countries pushing for an end to a ban on commercial whaling, led by Japan.
The 33 to 32 vote, with one abstention, came as Australia prepared to present what it says is proof that Japan's scientific whaling program is cruel to the meeting of the International Whaling Commission in St Kitts.
Environmentalists have reported witnessing whales that took 30 minutes to die after being harpooned. However Japan insists these cases are exceptions, not the rule.
Resolution on ban
The moratorium on commercial whaling, introduced 20 years ago in a bid to stop whales being overhunted into extinction, was a win for environmentalists.
The narrow victory of the vote will not result in in the moratorium being overturned because it needs to be endorsed by 75 percent of IWC members.
The resolution, proposed by commission hosts St Kitts and Nevis, criticises the moratorium, saying it is no longer valid due to rising whale numbers, and blames whales for depleting fish stocks. It also said that non-government organisations are a threat.
The declaration hands Japan a political weapon, and allows it to argue that more states on the 70-nation IWC body believe the moratorium should be overturned.
As well as St Kitts and Nevis other states that joined Japan in agreeing with the declaration included Norway, Iceland and the Caribbean state of Grenada.
Earlier, an attempt by Japan to abolish the Southern Ocean whale sanctuary failed to secure majority support.
Inhumane deaths
Australian Environment Minister Ian Campbell is due to present a report detailing cruelty to whales to the commission later on Sunday.
Environmental group Greenpeace said it filmed a number of kills at close range during the last Antarctic whaling season, during which Japan's annual so-called scientific catch was doubled to just over 1,000.
Scientists from conservation group the International Fund for Animal Welfare (IFAW) analysed the pictures.
"We found that for one whale the time to death was over half an hour, we found that the average time to death was 10 minutes," said spokesman Vassili Papastavrou, speaking to BBC News.
He said two of the 16 cases involved death by asphyxiation, with harpoons entering the whales' bodies near the tail and holding the animals upside down in the water.
"It's simply impossible for the harpooner to hit the whale close enough to the brain to ensure a reliable clean kill in all cases," he said.
But Japan said these examples are not the rule, saying the time to death for most whales is less than 30 seconds.
"Japan takes the issue of time to death very seriously, and is working together with Norway to improve the humane side of whaling," said spokesman for the Japanese delegation Glenn Inwood.
Japan and Iceland conduct "scientific" whaling allowed by the IWC but critics say it is a "loophole" in the charter.
Norway rejects the moratorium on commercial whaling entirely. About 2,000 whales a year are taken by the three nations.