Some 1.1 million people have signed a petition saying it supported a trade fuelling wild elephants' slaughter.
The company said it prohibited sales of raw ivory that breached a 1989 international treaty but not of ivory ornaments produced before that date.
Spokeswoman Takako Kaminaga said the ivory trade on the Yahoo Japan Auctions site was "patrolled" 24 hours a day.
"If we find a sale was illegal, we cancel it straight away."
Late last year, the Environmental Investigation Agency, in Washington DC, said the site had auctioned more than 12 tonnes of ivory products, including whole elephant tusks, in 2012-14.
Fake documents had enabled traders to "legalise" more than 1,000 tusks a year since 2011, it said.
Individually owned tusks face no registration requirement in Japan, and the tusks are not marked in any way to ensure the documents are valid for the items being registered.
Poachers kill tens of thousands of elephants a year to meet demand for the material, despite the trade ban, according to the Convention on International Trade in Endangered Species and other groups.
In September, the US and China agreed to work toward nearly complete bans on the ivory trade, and Japan is increasingly isolated in its stance favouring continued sales.
The international environmental campaign group Avaaz addressed its petition to Yahoo chief executive Marissa Mayer, Manabu Miyasaka, chief executive of Yahoo Japan, part-owned by Yahoo Inc. and Softbank Corp, and "all other companies allowing ivory sales online".
"As global citizens, we are appalled that you allow ivory to be sold on your site/platform, fuelling elephant extinction," it said.
"We call on you to urgently stop all ivory sales from sites/platforms in Japan and all other markets."
Various other online commerce sites, such as Amazon, say they have already stopped such sales or advertising.
Yahoo Japan was in touch with the local environment ministry and other agencies on the issue, as well as with Yahoo and other shareholders, Ms Kaminaga said.
Asked if the company might alter its stance, she replied: "You can't say there's absolutely no intention to change."
Softbank said in a statement that it had no comment on the issue.
Yahoo Japan has said it will strengthen its policies to remove illegal ivory from its online marketplace.