In an interview this week with "The Washington Post," al-Khuza'i also accused Iran of taking over some Iraqi border posts and sending spies and saboteurs to destabilize the country.
Iran denies the claims, saying Tehran -- "despite the wounds and damages inflicted [on Iran] by the former Iraqi regime" -- is doing everything it can to help the Iraqi nation.
Yahia Said is a research officer who specializes in Iraq and other nations in transition for the London School of Economics and Political Science. He told RFE/RL that al-Khuza'i's statement was both unprofessional and undiplomatic:
"The statements of the minister of defense were, to put it mildly, unprofessional," Said said. "He named Iran as Iraq's enemy number one, essentially declaring war in diplomatic language. And regardless of what motivated him to say that, it was an unprofessional statement which was rightly rejected or not supported by the prime minister [Iyad Allawi]."
In response to al-Khuza'i's comments, Allawi said Iraq "does not have enemies [in Iran] in that sense."
Labid Abawi, deputy foreign minister for policy planning, says Iraq's concerns about border issues apply not only to Iran "but also for the other neighboring countries."
Iraqi Deputy Minister of Interior Adnan Hadi Asadi declined to comment on the situation on the Iran-Iraq border when contacted by RFE/RL.
Iran, the biggest Shi'a state in the world, has special relations and interests in Iraq, where Shi'a Muslims make up more than 60 percent of the population.
Ali Reza Nourizadeh is director of the Center for Arab and Iranian Studies in London. He said Iran is eager to influence the situation in Iraq and has many channels in which to do so, the most effective being former Iraqi emigres who spent long years in Iran.
Nourizadeh said the Center for Arab and Iranian Studies has interviewed several Iraqi officials who have expressed concerns about the loyalty of these former emigres.
"[Iraqi officials] are very concerned, you know. There are thousands of Iraqis, or half-Iraqis, who lived in Iran, and they were cooperating with Iranian intelligence during Saddam's [rule]. They all returned to Iraq [now]," Nourizadeh said.
Nourizadeh said there are no accurate figures on how many have returned. He said the Iraqi Governing Council issued them passports and identity cards but that their backgrounds were not properly checked first.
"When the Iraqi defense minister is saying that Iran is becoming Iraq's first enemy, he is speaking about the Iranian influence and saying what other politicians wouldn't dare say in public," said Nourizadeh.
More importantly, the militias of some Iraqi political parties were trained with Iranian assistance.
Said from the London School of Economics said that the Supreme Council for the Islamic Revolution in Iraq (SCIRI) has the most efficient military organization, which was trained with Iranian support.
"The Supreme Council for the Islamic Revolution in Iraq, for example -- SCIRI -- is definitely [strongly affected by Iran], and has very strong links with the Iranian establishment," Said said. "Especially its military arm [Badr Brigades], which has now been transformed into a political organization, which is [named] Badr Organization. People in Iraq believe that there are lots of Iranian military officers and security officers in that organization."
Said pointed out that Tehran has other possible ways to influence Iraq. Iraq is the historical center of Shi'a Islam, and the holy cities of Al-Najaf and Karbala are destinations for Iranian pilgrims. It is not difficult for Iran to infiltrate these pilgrims with its own agents.
"You know, there are tens of thousands of pilgrims that come to Iraq -- Iranian pilgrims -- and you often hear reports about Iranian agents being among them, being caught among these pilgrims," Said said.
Analysts say that with no unity among the political elite of Iraq, the future of Iraq-Iran relations looks uncertain.
Nourizadeh said the situation might become more distinct after Iraq's prime minister visits Tehran, planned for August. He said Allawi will have to convince Iran to pursue one policy toward Iraq.
"We should wait until Mr. Allawi's visit to Tehran. I mean, he had an invitation from [Iranian President Hojatoleslam Mohammad] Khatami. We should see whether when he goes to Tehran he would be able to convince the Iranian government that better they come up with one policy towards Iraq, not two or three policies," Nourizadeh said.
Nourizadeh said that, although Tehran officially supports stability in Iraq, he believes Iran's Revolutionary Guards and its own security agencies have their own agendas and are acting in contradiction of the official line.
Nourizadeh pointed that the presence of the U.S. troops in Iraq worries Iran and complicates its relations with Iraq. He said Iran faces a difficult geopolitical situation, with U.S. troops also based in neighboring Afghanistan.
Even more, he said, Iran is afraid Iraq might eventually become a democratic and secular state.
"I don't think that by just removing Americans from Iraq, the problem between Iran and the new government of Iraq will be solved," Nourizadeh said. "No. The Iranian regime [will be] unhappy to see a secular, prosperous, federal Iraq near Iran."