BAGHDAD — The top U.S. general in Iraq on Monday predicted an upheaval in the country as militant groups jostle to fill the vacuum left behind by the withdrawal of all American forces in the coming weeks.

Gen. Lloyd Austin, commander of U.S. forces in Iraq, said the threat from the Sunni extremist organization al-Qaida in Iraq could grow at the same time that Iranian-backed Shiite militias are also seeking to assert themselves.

“Al-Qaida 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. Meanwhile, Shiite militias based mostly in the south will pursue their efforts to expand their capabilities, Austin said.

“There’s likely to be setbacks, some tough times in the days ahead,” he told journalists at a briefing at the U.S. Embassy in Baghdad. “As we leave, we can expect to see some turbulence in security initially.”

But, he added, “I’m hopeful that the right things will continue to happen.”

Austin’s comments underscored the considerable challenges that Iraq faces as it looks ahead to the post-American era at a time when mounting regional instability risks exacerbating existing tensions in the country.

Militant groups on both sides of the sectarian divide have not been vanquished, Iraqi politicians remain as deadlocked as ever on key issues confronting the country’s future, and Iraqi security forces still lack many of the capabilities that would enable them completely to fill the shoes of the departing Americans.

Notably, they do not have the capacity to mount a credible defense against any external threat to the country’s borders, a key concern of Iraqi leaders given the building unrest in neighboring Syria and the mounting tensions between Iran and the West.

Austin said he thought it likely that the Iraqi government would revisit the question of allowing a small force of U.S. trainers to return to the country after the withdrawal to focus on building the Iraqi army’s defensive capabilities. “If I were them, I would ask for help because we are the best in the world,” he said. But no negotiations are expected until after the withdrawal is complete, he said.

“This is not an end point,” he said. “We really intend to remain engaged in Iraq.”