Kurdish forces and al Qaeda-linked groups have for weeks fought over territory, with the Kurds taking over a key border point late last month.
But with the likelihood of more fighting to follow, Baghdad is worried of militants securing a wider corridor between eastern Syria and western Iraq.
"This border point is significant for both al Qaeda, and the (Syrian) Kurds," said Ali al-Haidari, a Baghdad-based security analyst. "At the same time, it threatens the Iraqi government's security as well."
"For al Qaeda, it is a border point through which they smuggle explosives, fighters and suicide bombers."
Iraq and Syria share a 600-kilometre border, and militant and Kurdish forces have for weeks fought fierce battles to the frontier's east, culminating with Kurdish fighters seizing the Al-Yaarubia crossing in late October.
Iraq's security forces reinforced their side of the border as the clashes raged in a bid to prevent militants from retreating into the northern Iraqi province of Nineveh.
The clashes do not directly threaten Bashar al-Assad, Syria's embattled president who has fought against an armed rebellion for more than two years.
But their proximity to Iraq and the strategic importance of the border point are the latest example of the Syrian civil war's potential spillover into Iraq.
"If it (Al-Yaarubia) fell into the hands of the Al-Nusra Front or other terrorist groups, our area would be in danger," said Naif Sido, the mayor of Snoni, an Iraqi town near the border.
Sido said security forces - both from the central government as well as Iraq's autonomous Kurdish region, which are often at odds - and local officials were holding weekly meetings to keep tabs on the situation.
Al-Nusra and the Islamic State of Iraq and the Levant (ISIL), both linked to al Qaeda, have increasingly fought against Kurdish forces in northern Syria, in Hasaka, Aleppo and Raqqa provinces.
Their aim, analysts say, is to establish control of key border points to ensure easier transit of fighters and equipment.
The militants also see Iraq and Syria as one large, contiguous battlefield.
"It's an ideological thing for them," said Aymenn al-Tamimi of the Middle East Forum think-tank.
Tamimi said ISIL in particular "sees Iraq and Syria as one battleground. It's part of the wider project of achieving the first goal of building an Islamic state in Iraq and Syria."
He noted that borders had been a focus for militant groups seeking to establish secure supply lines for reinforcements and military supplies.
And he warned that the Kurds' seizure of Al-Yaarubia did not mean the fighting was over.
"It's not going to stop," Tamimi said. "It's still going to be a pretty bad situation for the Iraqi government."
Iraq has long voiced concern over the impact of the bloodshed in Syria, al Qaeda's expanding role in the conflict and the potential spillover of the violence.
Unrest in Iraq has surged dramatically in recent months - more people died in October than in the first three months of 2013 combined - which officials and diplomats say is partly due to the conflict in Syria.
The war across the border, they say, has emboldened Sunni militant groups linked to al Qaeda and opposed to Iraq's Shia-led government.
ISIS has "succeeded in rebuilding some of its capacity in some areas (of Iraq)," Iraqi deputy national security adviser Safa Hussein told AFP.
Hussein said the main reason for the group's resurgence was the conflict in Syria, noting: "Now they have an open border, and strong - very strong - allies in Syria, and finance and weapons are almost open to them."
"They (militants) realise that the battle with Assad is a long battle," he continued. "If you like, the intermediate goal is having control of those key areas, or areas they think are key to their strategy."
Al Qaeda chief Ayman al-Zawahiri has ordered the Iraqi faction to stop meddling in Syria and anointed Al-Nusra to carry the network's banner in the war. But ISIL continues to issue statements under its name.
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