Major General Jabbar Yawir said an Ansar-allied group calling itself the "Kurdistan Brigades of Al-Qaeda" has repeatedly attacked Iraqi Kurdish forces in the region around the border town of Penjwin.
"The forces sent shall be in two brigades," he told AFP in the Kurdish city of Sulaimaniyah. "Some will reinforce army units and border checkpoints and some will mount patrols in the region to ambush the enemy."
The peshmerga are former Kurdish separatist guerrillas that have been incorporated into the Iraqi and Kurdish armed forces in the four years since a US-led invasion toppled the dictator Saddam Hussein.
The Kurdish autonomous region is regarded as relatively peaceful compared to central and southern Iraq, where attacks by Islamists and Saddam loyalists have provoked a civil war between Sunni and Shiite factions.
But the Kurdish Islamist group Ansar al-Islam continues to operate in the region, and US commanders have accused neighbouring Iran of sponsoring both Sunni and Shiite armed groups in a bid to foment unrest.
On Wednesday, a powerful truck bomb exploded in front of the Kurdish interior ministry in Arbil, killing at least 14 people. That attack was claimed by the "Islamic State of Iraq", an Al-Qaeda front organisation.