Mr Koizumi said he would take two weeks off in the first month of his child's life. The baby is due later this month.
It will be the first time a Japanese cabinet minister has taken paternity leave.
In Japan, both men and women are entitled to take up to a year off work when their child is born.
But only 6% of fathers did so in 2018 because of pressure to continue working. The figure for women was 82%.
"I intend to take a total of two weeks of paternity leave in the three months after childbirth, during which the mother bears the heaviest burden, on the condition that I prioritise my official duties and thorough crisis management, as I have done," Mr Koizumi, 38, told reporters on Wednesday.
He said he would be using more emails and video conferencing, and could ask his deputies to represent him during at business meetings as needed.
But Mr Koizumi added that he would not skip "important public activities", such as parliamentary sessions.
He has been discussing the idea of taking paternity leave since last year, triggering heated debates.
Mr Koizumi said at the time: "Japan is rigid and outdated because society is caught up with fussing over pros and cons simply because I said I would consider [it]."
Mr Koizumi is married to French-Japanese news presenter Christel Takigawa, 42.
He is the second son of popular former Prime Minister Junichiro Koizumi, and is seen as a rising star in Japanese politics.