Shinjiro Koizumi, a media-savvy 38-year-old married to a former television anchorwoman, told a ministry meeting it had been a difficult decision to balance his duties as minister and his desire to be with his newborn.
"I want to take a total of two weeks off flexibly, making exceptions for important public duties," he said, adding he hoped his decision would help change perceptions and encourage other fathers to follow suit.
He will not take the weeks off consecutively and said he expected to work remotely or have shortened days during the leave period -- which will be spread over three months from his child's birth.
The government's top spokesman backed the move, saying it was "important to create a conducive work-place atmosphere and social acceptance and support for men to ask for and take parental leave."
Chief Cabinet Secretary Yoshihide Suga told reporters that he hoped Koizumi's decision would have a positive impact on attitudes to male parenting.
There are no official records on whether cabinet ministers have previously taken parental leave, but Koizumi is the first to publicly announce he is doing so.
'Paternity harassment' cases
The son of a former Prime Minister, Koizumi was named environment minister in a cabinet reshuffle in September, becoming the third-youngest Japanese minister since the end of World War II.
He has been closely scrutinised as a potential rising star in the government, with his comments and behaviour subject to intense media dissection.
By law, Japan offers comparatively generous parental leave to employed workers.
Both parents can take up to a year off, with additional renewable six-month periods if a nursery place is unavailable.
But only six percent of fathers take parental leave, compared to more than 80 percent of mothers who use their allowance beyond the mandatory eight weeks after birth.
And of those men who take any leave, more than 70 percent are away for less than a fortnight.
Activists say that is the result of pressure from employers and a society that prizes long work hours.
A handful of men have sued their employers alleging they were subject to what is known in Japan as "pata-hara", short for paternity harassment, after taking parental leave.
The issue is a particular concern given Japan's birthrate, which in 2018 was one of the world's lowest -- and far below the rate the country needs to maintain its population.
There are diverse causes for the problem, some of which the government has sought to address by increasing nursery spaces and encouraging women to return to work after having children.