Japan typically accepts just a few dozen refugees a year out of thousands of applicants, and its borders are currently closed to virtually all foreign visitors to prevent Covid-19 infections.
But Kishida said the country would now "proceed with a plan to welcome people from Ukraine who have fled to third countries" in a bid to "demonstrate our solidarity with the Ukrainian people at such a crucial moment."
Kishida's remarks came after he held talks with the prime minister of Poland, which is hosting many of the more than 800,000 refugees who have fled Ukraine since the invasion began.
Kishida said Japan expected to first accept those with relatives or friends in the country, "but beyond that, we will respond from a humanitarian perspective," he added without setting a specific cap on arrivals.
He said refugees would be processed outside of the current border regime that bars foreign tourists and limits overseas arrivals.
There were no immediate details on how long refugees might be able to stay.
In 2020, Japan accepted just 47 refugees and 44 people on humanitarian grounds out of nearly 4,000 applicants, and rights groups have long accused Tokyo of doing too little to help those fleeing conflict.
Kishida said he had informed countries neighbouring Ukraine that are currently receiving refugees of the decision.
Japan has also backed international moves to sanction Russian and Belarusian individuals, exports and financial institutions while offering Ukraine loans and emergency humanitarian aid.
