One Iraqi border guard was killed and two others were wounded, he said. A doctor at a nearby hospital confirmed the toll.
The Syrian side of the Al-Waleed border crossing remains under the control of the regime of President Bashar al-Assad, but rebels fighting his rule have sought to take control of it over the course of several months.
Iraq has sought to avoid publicly taking sides between Assad's forces and the opposition, but western powers accuse Baghdad of turning a blind eye to flights through its airspace allegedly carrying military equipment for the Syrian regime. Iraq denies the charges.
More than 94,000 people have been killed and some 1.6 million Syrians have fled the country since the conflict erupted in March 2011, after Assad cracked down on pro-democracy protests, according to the Syrian Observatory for Human Rights.