But a forensic expert in the city said on Friday the body did not match the description of captive Shosei Koda.
"The information we received from the Iraqi government is that the possibility is very low that the body is of Mr Koda," Foreign Minister Nobutaka Machimura said.
"Japan is acting on the assumption that he's still alive and we will continue our efforts to rescue him," he said.
Earlier, while the Japanese government was trying to confirm whether the body was that of 24-year-old, Mrs Koda and her eldest son, Maki, 26, cut short their visit to Tokyo to return to the family's home town of Nogata, in the southern prefecture of Fukuoka.
"Of course they were shocked when I told them [an Asian body had been found], but Mrs Koda said she could not bring herself to believe the news," Tatsuya Yoshioka, an official of the Peace Boat charitable foundation, which is supporting the family, told Aljazeera.net.
German news agency DPA reported that the head of a medical facility in Tikrit claimed a body "with the characteristics of an Asian" had been recovered with "clear gun wounds to its head and chest".
Clinging to hope
"[Mrs Koda] said that because the reports have not yet been confirmed and are, at this point, only rumours that are not 100% certain, she will not give up hope," Yoshioka said. "They are being realistic and are just trying to keep strong."
Peace Boat will continue to send messages to Arab media outlets appealing for the release of Koda, he added.
The captors have demanded the
withdrawal of Japanese troops
In a press conference in Tokyo earlier on Friday, Mrs Koda said her son had only travelled to Iraq to help local people.
"I think he was just doing his best to make a difference and that he wanted to find a role he could play to further world peace," she said.
The family had not been aware that Koda was planning to go to Iraq, believing that he was studying English in New Zealand and planning to return to Japan to take up a course in nursing.
There were also reports that he worked casually in Israel for two months before crossing into Jordan and Iraq, but the first his family knew of this was when officials of Japan's Foreign Ministry called to say they had lost track of his whereabouts after he entered Iraq.
On Wednesday evening, video images of Koda kneeling before members of an armed group headed by Abu Musab al-Zarqawi were released on the Internet. The group threatened to behead Mr Koda unless Tokyo withdrew 600 troops based in the southern city of Samawa.
"I believe that he will come back alive and that he will achieve something that will really help the world"
mother of Shosei Koda
A 48-hour deadline passed at around 2:00am on Friday in Japan, with the government stating that it had no intention of ordering the Self-Defence Forces to leave Iraq.
'Born to prove'
"I named my son Shosei, with the characters of the name meaning 'born to prove his existence in the world' and I believe that he will come back alive and that he will achieve something that will really help the world," a tearful Koda told Aljazeera.net.
"We assume that he didn't tell us he was planning to go to Iraq because he knew we would be opposed and he did not want to burden us financially either," she added. Her husband, 54-year-old Masumi, is seriously ill and unable to work or travel far.