The China Post news staff
They shouted slogans against Ma, who insists that the Tiaoyutai islands, which the Japanese call Senkaku, belong to the Republic of China on Taiwan.
The Japanese claim sovereignty over the tiny islets some 50 miles northeast of Yilan. So does Taiwan.
The protest took place while Ma was meeting a group of ruling Liberal Democratic Party lawmakers at the Diet House to exchange views of issues of mutual concern to Japan and Taiwan.
Later in the afternoon, Ma spoke at Doshisha University in Kyoto. He broached his Asia policy, stressing that Taiwan wouldn't be a "troublemaker" in the region.
Washington considers Taiwan under the Democratic Progressive Party government a "troublemaker."
"If I were elected," Ma said, "I'll see to it that Taiwan, at the very least, won't be a troublemaker. Taiwan will be a peace-maker."
Ma arrived in Tokyo Wednesday for a three-day visit. He is expected to return to Taipei today.