Koike, a former television newsreader is known for sharing Abe's views on North Korea.
"The security environment surrounding our nation remains serious, especially after North Korea's ballistic missile launches and its nuclear experiment," she said.
Fumio Kyuma, the former defence minister, had come under intense criticism from atomic bomb survivors, opposition politicians and fellow members of the cabinet following the comments over the weekend.
Professor Jeffrey Kingston, a specialist in Asian affairs at Temple University in Tokyo, said Kyuma "had become a huge political liability to Abe, who is already very unpopular and who didn't need this".
He "acted quickly this time, perhaps because he wants belatedly to demonstrate he has the leadership people think he doesn't have. But it's a little too late," he said.
The row came as Abe struggles to persuade voters of the need for a more assertive foreign policy in the face of a nuclear-armed North Korea, when many seem to be more concerned about domestic issues such as pensions just a few weeks before elections for the upper house of parliament.
Support for had already been damaged by public outrage over the government's mishandling of pension records.