The distraught father of a Japanese hostage believed executed by his militant Islamist captors has told how his mind had gone "totally blank" when he heard the news of his son's death.

"I thought 'Ah, this has finally happened' and was filled with regret," Shoichi Yukawa said on Sunday, hours after a video appeared online claiming that self-styled military contractor Haruna Yukawa has been executed.

"I went totally blank, I was only sorry... I had no words to say," the 74-year-old said.

The apparent announcement of the 42-year-old's death came days after the Islamic State group published a video in which it threatened to kill him and freelance journalist Kenji Goto unless Japan paid a $US200 million ($A248.23 million) ransom within 72 hours.

That deadline passed on Friday, with Tokyo saying it was still making frantic efforts to contact the jihadists.

Late Saturday a three-minute video was released showing a still image of Goto holding a photograph of a decapitated body said to be Yukawa.

In the accompanying audio recording a man claiming to be Goto blames Japanese Prime Minister Shinzo Abe for Yukawa's killing, and demands the release of an Iraqi woman sentenced to death in Jordan for her part in multiple bombings.

Shoichi Yukawa on Sunday repeatedly apologised to Goto, who was understood to have travelled to Syria to try to free his son.

"We are very sorry for causing trouble" to the public as well as to Goto, the father said.

"We are deeply grateful that the government and others concerned have made their utmost efforts."

The father said his son had felt as if Goto, 47, was his "big brother".

"My son told me all the time that he is a sincere, very courageous and gentle man.

"I feel it very painful that Mr Goto worried about Haruna, went there and risked his own life and then was kidnapped and threatened this way," he said.

"I had been hoping something like this wouldn't happen, but it finally did.

"If I could see him again, I would hug him with all my strength," he said.