The popular "Oishinbo" ("Gourmets") drew criticism in late April when it showed its main character, a newspaper reporter, having a nosebleed after visiting the tsunami-crippled nuclear plant.
In the same edition, another character -- the real-life former mayor of a nearby town -- says: "There are many people who have the same symptom in Fukushima. I want to say we should not live in Fukushima as it is now."
They charged the comic would add fuel to rumours that have scared people away from farm and fishery products from the region, even if they comply with safety standards.
Unlike comics in the West, manga are treated as a serious art form in Japan, on a par with novels, and are widely read among the adult population.
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They often take complex or current issues as their subject matter and can be influential in shaping public opinion.
But in the latest edition published today, the chief editor of the weekly magazine that runs the strip acknowledged it had caused alarm.
"We have received a lot of criticism and complaints. As the editor in chief, I am aware of my responsibility for the unpleasant feelings this has generated," said Hiroshi Murayama.
"We will review the language used and will take on board the criticism that has been made."
The comments came after Prime Minister Shinzo Abe weighed in during a weekend visit to Fukushima, where the coastline was wrecked by the March 2011 earthquake and tsunami.
In front of media cameras, the premier tasted cherries and helped plant rice seedlings at farms in the main city of Fukushima, some 60 kilometres away from the plant.
Although the natural disaster that sparked the accident left more than 18,000 people dead, the nuclear catastrophe -- the world's worst in a generation -- is not officially recorded as having directly killed anyone.
While most scientific opinion says there is minimal risk to the population from the released radiation, there is widespread distrust of the government and regulators.