Baghdad ordered troops to shut the Traibil border post in the Sunni heartland province of Anbar, where protests erupted in late December after authorities arrested the bodyguards of a Sunni finance minister, local officials said.
"Our work has halted completely," Colonel Mahmoud Mohammed Ali, deputy chief of border police at the crossing told Reuters.
"There are no trucks, no passenger cars, and officials at the gate are not working."
Local Sunni officials in Anbar said the central government had closed the crossing to choke the local economy in an attempt to put pressure on protesters who have blocked a main highway through the desert province for more than two weeks.
Thousands of demonstrators are camped out on the highway near the Sunni stronghold of Ramadi, about 100km west of Baghdad, before the point at which it splits, with one road leading to Syria and another to Jordan.
The protests have become a major test for Maliki, a Shi'ite nationalist whom many Sunni leaders accuse of marginalising their minority sect, shoring up his own authority and pushing the OPEC country closer to Shi'ite non-Arab power Iran.
The latest turmoil erupted as conflict in Syria, where Sunni insurgents are battling President Bashar Assad who is backed by Shi'ite Iran, fuels regional sectarian tensions and tests Iraq's own fragile cross-communal and ethnic balance.
Since the last US troops left Iraq a year ago, the government made up of majority Shi'ite, Sunni and ethnic Kurdish blocs has been deadlocked in a crisis over how to share power.