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A sobbing Junko Ishida told foreign journalists her son was a humanitarian who worked to better the lives of children.
"I say to you people of the Islamic State, Kenji (Goto) is not your enemy. Please release him," she said.
"Kenji was always saying 'I hope to save lives of children on battlefields'. He was reporting war from a neutral position."
The Islamic State movement has threatened to kill her son, a respected freelance journalist, and Haruna Yukawa, a self-employed contractor, whom they have been holding since last year, if the Japanese government does not pay the ransom.
The group released a video earlier this week in which Goto and Yukawa apparently knelt in a desert as a British-accented man loomed over them brandishing a knife.
"You now have 72 hours to pressure your government into making a wise decision by paying the $200 million to save the lives of your citizens," he said.
Tokyo believes the deadline will expire at 2:50 pm (0550 GMT) on Friday.
REUTERS/Toru Hanai
"I've been sobbing for the last three days, feeling very sad," Ishida said. "It is impossible to describe this feeling."
Asked if Ishida wants the Japanese government to pay the ransom, she replied: "Yes, I very much hope so.
"Japan has maintained a friendly relationship with Islamic nations.
"The time remaining is scarce. I beg you Japanese government officials, please save Kenji's life."