In an interview to Aljazeera's correspondent in Tokyo on Wednesday, he said, "Koda is a civilian who has nothing to do with the Japanese government or the troops in Iraq.
"Therefore, on behalf of the Japanese people, I call for the release of Shosei Koda."
Machimura said "for many years, Japan has actively cooperated in building Iraq, including the building of schools and hospitals".
The Japanese foreign minister cited the example of the "conference to rebuild Iraq that was held in Tokyo two weeks ago, in which 53 countries and four international organisations participated".
Machimura told Aljazeera "the Japanese people were surprised (by Koda's capture) and they hope he will be released as soon as possible".
Japan's troop contingent polices
a peaceful stretch of the south
Saying that a lot of nations are friendly towards Japan, he said, "We've asked our ambassadors in many countries to help in releasing the Japanese captive."
At the same time he said, "We will continue our support to build the Iraqi government. We send aid to the Iraqi people. They are human beings in the first place and that is the main reason behind our presence in Samawa [in southern Iraq]".
Earlier, on Tuesday, Jordanian fugitive Abu Musab al-Zarqawi's al-Qaida Organisation of Holy War in Iraq group said it was giving Japan 48 hours to withdraw its troops from Iraq "or this infidel will meet the same fate as ... the other infidels".
A video posted on a website often used by the group showed Koda, with long hair and a thin beard, seated in front of three masked men and a black banner bearing the group's name.
"Koda is a civilian who has nothing to do with the Japanese government or the troops in Iraq"
Japan's Foreign Minister
Japan has sent about 550 non-combat troops to southern Iraq to carry out what it calls humanitarian and reconstruction work.
Koda, 24, whose family comes from Fukuoka in southern Japan, has appealed to Japanese Prime Minister Junichiro Koizumi to save his life by meeting the demand of his captors" the withdrawal of the [Japanese] Self-Defence Force contingent.
But Koizumi said on Wednesday he will not withdraw troops from Iraq.
The Iraq deployment move was
opposed by many Japanese
"We cannot tolerate terrorism and we will not give in to terrorism," Koizumi said. "We will not withdraw the Self-Defence Force."
The incident is a political challenge for Koizumi, who decided to send Japanese troops to Iraq despite strong public opposition.
On the diplomatic front, Foreign Minister Machimura telephoned interim Iraqi prime minister Iyad Allawi on Wednesday to ask for help to win Koda's release and was told action had already been taken, the Japanese foreign ministry said in a statement. No details were given.
Also, according to Aljazeera's Tokyo correspondent, Japan's deputy foreign minister has left for Jordan's capital Amman as a first step in an attempt to seek Koda's freedom.
For their part, Koda's family has written to Koizumi and Machimura, asking for help to secure his release.
"As his parents, we
are hoping that our second son, who left in high spirits, will return
in high spirits"
father of Soshei Koda
"As his parents, we are hoping that our second son, who left home in high spirits, will return in high spirits," Koda's father Masumi said.
In the dark
Koda's family has told Japanese public broadcaster NHK that he had gone abroad in January and started a working holiday in New Zealand in July. They had not been told of his trip to Iraq.
Koda's mother Setsuko, wiping tears from her eyes, said: "What will they get by killing my young son?"
Media reports said Koda was working at a hotel in Amman and had taken a bus to Iraq last week despite being warned not to by colleagues.
However, al-Qaida Organisation of Holy War in Iraq, which is holding Koda, said the Japanese worked with his country's forces in Iraq.