Kazuya Maruyama, a lawyer-turned-lawmaker in Prime Minister Shinzo Abe's ruling party, apologized hours after making the remark at a parliamentary constitutional panel, saying it was misleading.
"Today, America has a black person as President. A person who inherits black people's blood. Frankly speaking, they were slaves," he said Wednesday, then went on to explain how civil rights improved in the US.
"Back at the beginning of US history, it would have been unthinkable that a black person, a slave, would become President. That's how dynamic a transformation this country makes."
The president has spoken often about America's racial history and what it means for him to be the first black US president.
Japanese often exercise self-restraint or overreact to certain words and actions to avoid controversy. A zoo last year was accused of insulting British royals by naming a baby monkey Charlotte for the British princess, but it kept the name as the public's choice.
The US Embassy declined to comment.
Maruyama denied any racist intent.
The remarks were made as he questioned experts about a revision to Japan's constitution, which has never been amended since it was drafted by the United States during its post-World War II occupation. He noted there would be no problem if Japan becomes America's "51st state" and that would allow people from "the state of Japan" to become US president.
He quit the constitutional panel Thursday but refused to resign as lawmaker.
Several lawmakers in Abe's party have recently been hit by scandal. A communications minister was criticised for warning television networks their licenses could be stripped if they aired "biased" political news.
A parliamentarian who admitted to adultery resigned. The economy minister quit over a bribery allegation.
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