However, Kim said that improving bilateral relations between the two countries will depend on whether Japan can make practical political decisions.
"The prime minister should know that just because he wants to and has made a decision, it doesn't mean he can or the leadership of our country will meet him," Kim was quoted as saying in the KCNA report in Korean.
"What is clear is that when Japan antagonises the Democratic People's Republic of Korea and violates its sovereign rights, it is considered our enemy and will become part of the target," Kim added.
The Democratic People's Republic of Korea is the North's official name.
Asked about the media reports on Kim's comment, Kishida reiterated the importance of a summit meeting to resolve bilateral issues such as the matter of Japanese citizens kidnapped by Pyongyang's agents decades ago.
"It is important to hold a top-level meeting to resolve the abduction issue and other problems. As I've been saying, we are approaching North Korea in various ways under my direct supervision," Kishida told a parliamentary session.
Later on Monday, Japan's top government spokesperson Yoshimasa Hayashi said North Korea's assertion that the abduction issue has already been resolved is "totally unacceptable", underscoring potential obstacles to amending ties.
Kishida has said he wants to hold talks with North Korean leader Kim Jong Un "without any preconditions" and is personally overseeing efforts to realise the first such leaders summit in 20 years.
An official at South Korea's foreign ministry, who asked to remain unidentified, said Seoul was in close talks with Tokyo on a range of issues related to North Korea including contacts between Japan and the North.
Kim's sister, who serves in the ruling Workers' Party, last month said Kishida may one day visit Pyongyang.
"If Japan ... makes a political decision to open a new path for improving ties based on mutual respect and respectful behaviour, it is my view that the two countries can open a new future," KCNA quoted her saying.
