The new Iraqi government's decision to strike cooperative agreements with neighboring Iran shouldn't necessarily sound alarms, but such reports should be watched closely as a potential harbinger of political winds in the region, say military and cultural experts who spoke with FOXNews.com.

Last week, Iraqi Prime Minister Ibrahim al-Jaafari met with senior Iranian leaders President-elect Mahmoud Ahmadi Nezhad, Ayatollah Ali Khameneh'i and outgoing President Mohammed Khatami. In the meeting with Khatami, the two sides pledged to work together to restore stability to the region.

Their meeting was also followed by reports in the region this week that the two countries had reached agreement to build oil pipelines from the Iraqi port city of Basra to refineries in Iran.

Al-Jaafari's trip came on the heels of his defense minister's sojourn there more than a week earlier, the headlines from which seemed to suggest a new era in military cooperation between the two neighbors.

During his visit to Iran, Iraqi Defense Minister Saadoun al-Duleimi (search) told reporters at a joint news conference with his Iranian counterpart, Ali Shamkhani, that it was time to "open a new page in our relations against the painful page of the past."

Al-Duleimi was referring to the bloody, inconclusive 1980-88 Iran-Iraq War, which killed a million people on both sides.

The next day, Reuters reported that the two had signed a pact according to which Iraq would accept military training and other assistance from Iran.

"Nobody can dictate to Iraq its relations with other countries," al-Duleimi reportedly said when asked if the agreement would anger Washington.

By Monday, al-Duleimi denying that the pact would include military training assistance.

Asked if Shamkhani had misrepresented the pact, al-Duleimi replied: "He has the right to mention what he wants. We, as Iraqis, are not responsible for that."

Al-Duleimi did confirm that the pact included an Iranian aid package worth $1 billion, some of which would be going to the Defense Ministry, according to the Washington Post.

"It's a diplomatic slap in the face, but I'm not sure how much of a diplomatic slap in the face," said Michael Rubin, a Middle East specialist with the American Enterprise Institute.

He added that the United States may not like collaboration between Baghdad and Tehran, but Iraq is a sovereign nation and should be reaching out to its neighbors.

Abbas Khadim, an Iraqi who lectures in Islamic studies at the Graduate Theological Union in Berkeley, Calif., agreed.

"There is no way we can sever the relations between Iraq and Iran," said Khadim. "They are joined at the hip, as they say, because of the long-time religious and traditional connections.

"Right now, the Iraqi government is trying to prove that it is absolutely not the puppet of the Americans," he added. "I think it's a smart idea to build relations with Iran based on cooperation — and it gives Iran assurance some assurance that Iraq won't be a hostile neighbor."

The U.S. State Department may have doubted the purported Iran-Iraq military pact. Spokesman Tom Casey said July 9 that the department was "fairly uncertain as to what may or may not have happened."

However, he added: "We certainly would encourage Iran to play a positive and productive role in helping the Iraqis, as we are trying to do, establish a free democratic system and to build a prosperous and peaceful country."

Iran is still on the State Department's list of nations that sponsor terrorism, and has been criticized by the Bush administration over its nuclear-energy program, which U.S. officials believe is a front to develop nuclear weapons.

The administration has also accused Iran of meddling in Iraqi politics.

Marine Corps Col. (Ret.) Thomas Hammes, author of "The Sling and the Stone: War in the 21st Century," said the U.S. must ease up on those concerns if it wants the new Iraqi government to be free and legitimate.

Hammes said if Iranians and Iraqis want to train together, there is little the administration can do about it.

"That's something we have to work out with the Iraqi government," said Hammes. "If they are sovereign, they can invite in whom they choose to invite in. Both political parties [in the U.S] can make hay out of this ... but it is more of a domestic political issue, I see, than an international issue."

Since the fall of Baghdad, the U.S. has been in charge of training the Iraqi military. The Bush administration and Pentagon agree that American forces will not leave the country until Iraqi soldiers can carry out the bulk of security missions on their own.

The current Iraqi government is dominated by Shiite Muslims, many of whom are affiliated with the Supreme Council for Islamic Revolution in Iraq (SCIRI).

The SCIRI militia, the Badr Brigade (search), was trained in Iran as a resistance movement against Saddam Hussein, fought on the Iranian side during the war and now works unofficially to crack down on the Sunni-led insurgency in Shia areas of the country.

Iraqi Sunni Muslims have accused the Badr Brigade and its offshoot, the elite Wolf Brigade, an official security force of the Interior Ministry, with abusing and even killing Sunnis in recent months.

News of cooperation between Shia Iranians and Iraqis may be seen by Sunnis as a foreshadowing of religious bias and alienation, experts say, which the U.S. had hoped the new Iraqi government would avoid. But the extent that these fears will be realized is anyone's guess.

"The Sunni may freak out about it," said Steven Schwartz, author of "The Two Faces of Islam: the House of Saud from Tradition to Terror. "Of course, they will make it sound like there will be an imminent theocracy."

However, Schwartz does not believe that Iraq wants to become another Iran, ruled by mullahs. And he does not think Iran has sinister motives.

"I don't believe Iran has any interest in creating any problems for Iraq," he said.

Rubin, who will be traveling to Iraq in August, suggested that the Iraqis are testing their independence.

"The Iraqis have shown themselves, time and time again, that they are not Iranian agents," he said. "If we are a bit more respectful of Iraqi sovereignty, the Iraqis may not try to poke us in the eye so often, and hopefully we won't overreact."

The Associated Press contributed to this report.