Maj. Gen. Kevin Bergner said he welcomed the Iraqi government's commitment to target criminals in Iraq's second-largest city but he concedes there are challenges.
He said most of the Iraqi troops "performed their mission" but some "were not up to the task" and the Iraqi government is investigating what happened.
The government was surprised by ferocious resistance from followers of Shiite cleric Muqtada al-Sadr to the offensive.
The Iraqi campaign in Basra also faced desertions and mutiny in government ranks before a cease-fire order by al-Sadr on Sunday.
Meanwhile Wednesday, an Iraqi commander led a convoy of troops firing into the air Wednesday in a show of force in a militia stronghold that has seen some of the fiercest fighting in the southern city of Basra.
The move came a day after Prime Minister Nouri al-Maliki returned to Baghdad from Basra politically battered after Iraqi security forces failed to crush the militias as promised.
The Iraqi troops met no significant resistance Wednesday, although an Iraqi cameraman for the U.S.-funded Alhurra TV station was shot, as they set up checkpoints on the edge of the sprawling Hayaniyah district in central Basra and drove through the main streets, according to witnesses.
Officials with Muqtada al-Sadr's Mahdi Army militia in Basra said they tolerated the government move in compliance with a cease-fire order by the radical Shiite cleric under an Iranian-brokered deal to end the fighting.
But they warned they would fight back if security forces resumed large-scale raids and arrests without warrants.
A Mahdi Army spokesman known as Abu Liqa al-Basri said Iraqi forces had raided some houses in Hayaniyah, then withdrew to a single main street.
He said people were moving freely in the sprawling area and gunmen were keeping a low profile. But he accused the Iraqi security forces of creating a "crisis of trust" by violating al-Maliki's order not to detain people without warrants.
"Al-Maliki's orders are the safety valve," he said. "If the Iraqi army continues in its provocative raids, the consequences will be bad."
The situation remained calm but tense in the oil-rich city 340 miles southeast of Baghdad.
Bergner, the U.S. military spokesman, said the vital port area had been secured with the arrival of two Iraqi army battalions and Iraqi marines.
He also said the Iraqi government had informed the U.S.-led coalition in advance that it planned the offensive, but he declined to give a timeframe.
A roadside bomb targeting a U.S. convoy also exploded near a restaurant in Baghdad's main Shiite district of Sadr City, killing at least three Iraqi civilians and wounding 13, police said.
The stakes were high after al-Maliki flew to Basra for a week to personally oversee the crackdown that began on March 25, promising "a decisive and final battle."
U.S. and Iraqi officials have insisted the target of the crackdown was not the Sadrist political movement but criminals and renegade militias. But the Sadrists believed the operation was aimed at weakening their movement before provincial elections this fall.
Fighting eased after al-Sadr called his fighters off the streets Sunday under a deal brokered by Iran after clashes spread to Baghdad and other southern cities amid anger over the Basra crackdown.
But the gunmen refused to surrender their weapons and several Basra neighborhoods appeared to remain under militia control - developments that left the radical Shiite cleric in a position of power and al-Maliki politically battered.
In issuing his cease-fire order, al-Sadr also called on the government to stop "illegal and haphazard raids" and officials said al-Maliki had agreed that arrests should only be made with warrants, indicating that a deal was reached between the two parties after intense negotiations.
Harith al-Edhari, the director of al-Sadr's office in Basra, said the government was not holding up its part of the deal.
"So far we are adhering to the orders of our commander to hide weapons and refrain from holding arms in public, but the field officers of the Iraqi army are not abiding by the prime minister's instructions not to raid houses of al-Sadr's followers and the Mahdi Army," he said.
Lt. Gen. Mohan al-Fireji, who heads the joint Iraqi army-police forces in the area, led the convoy of armored vehicles into Hayaniyah at about 9:30 a.m. and the troops fired their weapons into the air to clear traffic.
The wounded Iraqi cameraman for Alhurra TV, Mazin al-Tayar, told The Associated Press at the hospital that he was shot at twice while traveling with the convoy to film the event.
One bullet missed but the other struck his left leg, leaving his clothes and his camera soaked in blood. He was in stable condition.
The Basra joint operations center also announced that Iraqi soldiers had detained two suspected militia figures in the Qibla area, but a gun battle broke out during the raid and an Iraqi army vehicle was set on fire.
The Interior Ministry spokesman, Maj. Gen. Abdul-Karim Khalaf, said Tuesday that 200 people had been killed, 600 wounded and 170 suspects detained during operations in Basra and he reiterated that an April 8 deadline for gunmen to surrender their weapons would be maintained.
The provincial governor, Mohammed al-Waili, also said the overall situation in the city was "very calm and stable" and a measure of normalcy was returning.
"We issued orders to all government employees to go to their offices starting from today and they will be obliged to work their full schedule," he said.
The faltering effort to drive Shiite militias from Basra has raised doubts about whether the Iraqis are capable of maintaining security in Iraq just a week before top U.S. commander Gen. David Petraeus is to brief Congress about prospects for further American troop cuts.
On Tuesday, Britain froze plans to withdraw about 1,500 soldiers from its 4,000-strong military force that is concentrated in the Basra area this spring and hand over more security responsibility to the Iraqis.
"It is prudent that we pause any further reductions while the current situation is unfolding," British Defense Secretary Des Browne told the House of Commons.
Suspected al Qaeda in Iraq insurgents, meanwhile, continued their campaign against fellow Sunnis who have joined forces with the Americans against the terror network.
Four of the U.S.-allied fighters were killed Wednesday and four others abducted at a fake checkpoint near Duluiyah, 45 miles north of Baghdad, police said.