The South Korean electronics giant had sought an injunction that would prevent the manufacture and sale of some of Apple's smartphones in a dispute over patent rights, the spokesman said.
In response to Samsung's claim made in 2011, Apple filed a lawsuit seeking a court ruling that Samsung does not hold patent rights and thus has no claim to damages over the issue, he said.
Similar lawsuits over the same technology were heard in the United States and South Korea, with a US court finding for Apple in August last year while a South Korean court sided with Samsung, the spokesman added.
A spokesman for Apple Japan declined to comment on the case.
The verdict is the latest chapter in a long-running global patent war between the smartphone giants, who have each accused the other of stealing intellectual property for their own products.
In a separate case, the Tokyo District Court in August rejected Apple's claim that Samsung stole its technology over synchronising a smartphone's music data with that on a computer.
The two companies are waging the patent fight in about 10 countries, and in Japan there are about a dozen cases pending, the Samsung spokesman said.