FORWARD OPERATING BASE CALDWELL, Iraq (CNN) -- Although America's top general in Iraq called al Qaeda "the wolf closest to the sled," he said sectarian fighting among militias fueled by Iran could be the biggest long-term challenge for Iraq.
Petraeus says Iran must prove it is no longer supplying weapons to Iraq militias.
"Militias could potentially be the long-term problem for Iraq, if you assume that we can continue to make progress against al Qaeda," Gen. David Petraeus told CNN's Jim Clancy near the Iranian border in Iraq's Diyala province.
Petraeus is in a "show-me mode," waiting to see if Iran honors a pledge to stop the flow of arms, money and training from Iran into Iraq that has helped both Shiite and Sunni militants.
"Al Qaeda remains the wolf closest to the sled, if you will," he said. "The enemy that is always bent on reigniting sectarian violence, causing the most horrific casualties, damaging the infrastructure in the most difficult way. So you cannot lose focus on al Qaeda."
But, Petraeus added, there was "no question" that Iranian arms were ending up in the hands of the Iraqi militias and there was "no debate" that six Iranians detained by the U.S. military in northern Iraq are Iranian Quds force members -- the Iranian unit the United States accuses of training and arming insurgents.
"There's no question, absolutely no question that Iran is providing advanced RPGs [rocket-propelled grenades], RPG 29s," Petraeus said.
"It has provided some shoulder-fired, Stinger-like air-defense missiles. It has provided the explosively formed projectiles and it has provided 244 mm rockets, in addition to mortars, mortar rounds and other small-arms ammunition."
Petraeus also said the Iranians "are implicated in the assassination of some governors in the southern provinces."
He said one indication the Quds force controls Iranian policy is that Iran's ambassador to Iraq, Hassan Kazzem Qomi, is a member of the group. Qomi, who has diplomatic immunity, could not immediately be reached for a reaction.
Petraeus said the Iranian ambassador has given his Iraqi counterpart assurances Iran would stop supplying and training Iraqi insurgents.
"They had two sessions," he said. "Numerous Iraqi leaders have gone to Tehran and asked that they stop very, very directly, stop the lethal assistance. There have been sub-ambassadorial meetings as well. And there have been assurances in return actually from Iran to Iraqi leaders and we are waiting to see if those assurances bear fruit or not, frankly.
"We are very much in the 'show-me' mode right now. We would love to see that."
Petraeus reiterated that Iranians detained by the United States recently in northern Iraq are Quds Force members. One of them was arrested recently in Sulaimaniya, Iraq, and five others were arrested in Irbil.
The U.S. military has intercepted caches of explosively formed projectiles -- a more sophisticated and powerful type of roadside bomb -- and other weapons from Iran in recent months, but Petraeus said stopping the regular flow of arms to the militias is a challenge.
Meanwhile Sunday, Iran reopened one of five entry points with Iraq's Kurdish region, and was in the process of reopening the other four, a Kurdish regional spokesman told CNN.
Hajj Umran, a border entry near Sulaimaniya had been reopened, and Iran will likely open the others -- one in Irbil, another in Sulaimaniya and two others in Khanaqin -- on Monday, said Kurdistan Regional Government spokesman Jamal Abdullah.
Iran closed its border with the Iraqi region nearly two weeks ago to protest the U.S. military's incarceration of an Iranian arrested in Sulaimaniya on September 20.
The U.S. military maintains Mahmoody Farhadi was arrested in the northern Iraqi city while posing as a businessman with a trade delegation and was in charge of Zafar Command, which is one of three units of the Ramazan Corps of Iran's Islamic Revolutionary Guard Corps - Quds Force.
The decision to reopen the entry points followed talks in recent days between the Iranian government and a delegation from Kurdistan Regional Government -- which traveled to Tehran on Thursday, KRG spokesman Jamal Abdullah said.
Abdullah said the KRG was involved in talks with Iran to resolve border issues prior to Farhadi's arrest.
Iraqi President Jalal Talabani blasted the United States for the arrest, saying Farhadi is a civil servant who was on an official trade mission in the region.
The other border points between the two countries remained open during the nearly two weeks Iran closed its border with the Kurdish region. E-mail to a friend