The top U.S. general in Iraq on Monday warned that violence there will probably increase after U.S. troops withdraw, setting the stage for a potentially rocky start to the post-American era in Iraq.

Gen. Lloyd J. Austin III, the commanding general for U.S. forces in that country, predicted that the threat from the Sunni extremist organization al-Qaeda in Iraq could grow as militant groups jostle to fill the vacuum that the departing Americans leave behind. Shiite militias backed by Iran will also seek to assert their capabilities, he said.

“As we leave, we can expect to see some turbulence in security initially, and that’s because you’ll see various elements try to increase their freedom of movement and freedom of action,” he told journalists at a briefing at the U.S. Embassy in Baghdad, just weeks from the planned departure of the last American troops.

Austin’s comments represent the clearest statement yet by a U.S. military commander that the United States is leaving unfinished business in Iraq — particularly at a time of mounting regional instability that risks exacerbating long-standing tensions.

Militant groups on both sides of the sectarian divide have not been vanquished, the country’s fractious politicians remain deadlocked on key issues, and the Iraqi security forces lack many of the capabilities that would enable them to fill the gaps left by the departing Americans.

Austin said conditions for a U.S. exit are better than at any point in the previous 81 / 2 years, but he said that “there will probably be unfinished business for many, many years to come.”

The U.S. military had hoped that as many as 20,000 of its troops would remain to continue to train Iraqi security forces, but an agreement on the terms under which the troops would stay foundered on the issue of whether the trainers and those assigned to protect them would be granted immunity from prosecution.

Though it is possible that the Iraqis will ask for additional help after the drawdown is complete, Austin said, no such request has been made.

Foremost among U.S. concerns is the risk posed by militant groups, including al-Qaeda in Iraq, which remains a potent threat in the north and center of the country and is capable of staging devastating attacks. Austin said the group is expected to try to take advantage of the United States’ departure.

“Al-Qaeda will continue to do what it’s done in the past, and we expect that it’s possible they could even increase their capability,” he said. “If the Iraqi security forces and the government of Iraq are able to counter that, it will be a good thing. If they can’t, they’ll continue to grow in capacity.”

At the same time, Iranian-backed Shiite militias, based mostly in the south and around Baghdad, are also expected to try to expand their role, in ways that could challenge the Iraqi government’s hold on power.

“These are elements that are really focused on creating a Lebanese Hezbollah kind of organization in this country,” Austin said. “As we leave, if those elements are left unchecked, they will eventually turn on the government, and they should be concerned about that.”

A particular worry for the United States, he said, is the threat that those militias could pose to the sizable number of U.S. diplomats who will remain at the fortified U.S. Embassy in Baghdad’s Green Zone. The Iranian-backed group Asaib Ahl al-Haq has kidnapped Westerners, and the Promised Day Brigade, controlled by anti-American cleric Moqtada al-Sadr, has been held responsible for many of the rocket attacks against the embassy in recent years.

Austin said he does not foresee a dramatic collapse in security, but he warned that containing the threats will depend on the response of the Iraqi security forces and the government.

“There’s likely to be setbacks, some tough times in the days ahead,” he said. “But I’m very hopeful we’ll stay on course.”

All American troops are scheduled to leave by the end of the year under a U.S.-Iraq security agreement signed in 2008, and with fewer than 20,000 now in the country, the withdrawal is on track to be completed by then, U.S. officials say.

Another concern for American and Iraqi officials is the Iraqi army’s inability to mount a credible defense against any external threat to the country’s borders at a time when unrest is spiraling in neighboring Syria and tensions are mounting between the West and another Iraq neighbor, Iran.

With F-16 fighter jets not due to be delivered until 2015 and only small numbers of tanks and other military hardware currently in their arsenal, the Iraqi security forces lack “very much of a capability at all to address an external threat,” Austin said.

Though the Iraqis need help, it is far from certain that they will ask for it, he said. And if they do, it is possible that they could seek assistance from other countries, he added, seemingly acknowledging that the United States might not be able to count on Iraq as a strategic ally in the future.

But he said he believes that Iraq wants to uphold close ties with the United States, and he pledged that America will continue to pursue that relationship.

“This is clearly not an endpoint,” he said. “We really intend to remain engaged with Iraq, and we look forward to having Iraq as a great strategic partner in the future.”