Sunni rebels have captured Iraq's biggest oil refinery after overnight clashes with Iraqi security forces, according to local sources, but a military spokesman denied it.

A journalist in Saladin province told Al Jazeera that Sunni rebels, led by the Islamic State in Iraq and the Levant (ISIL), had seized the refinery at Baiji, 43km north of Tikrit, on Saturday.

An unknown number of soldiers had been taken prisoner by the rebels after the fall of the facility, the journalist said.

The oil ministry did not comment on the report, and referred all enquiries to the defence ministry.

Rebels had withdrawn from the refinery on Friday after heavy clashes and retreated to Baiji's main town, which they already control.

State TV reported that Iraqi forces, backed by combat aircraft, had repelled four attacks on the refinery by ISIL fighters.

Iraqi security forces have largely halted the initial rapid advance by ISIL-led fighters, but the rebels continue to make gains.

On Friday, Sunni fighters captured the Qaim border crossing with Syria, 320km west of Baghdad, after a day of clashes that killed about 30 Iraqi soldiers.

The most recent gains by the Sunni rebels come as Shia fighters loyal to the powerful religious leader Moqtada al-Sadr rallied across Iraq, vowing to protect the capital Baghdad, and religious sites.

Both civil and religious leaders, including Grand Ayatollah Ali al-Sistani, have called on citizens to volunteer in the battle against ISIL-led groups, which have taken large parts of the country.