There were no immediate figures on casualties in the attack early on Sunday morning.
The attacks may signal that US occupation forces are readying for a fresh assault on al-Mahdi Army positions as negotiations between Muqtada al-Sadr aides and those representing Grand Ayat Allah Ali al-Sistani over control of the Imam Ali mosque are bogged down.
According to an Iraqi journalist based in Najaf, sporadic clashes between US occupation troops and al-Mahdi Army militia broke out several times on Saturday evening.
"The Mahdi Army is vowing to protect the sanctity of the holy shrines even if the keys are handed over to Shia religious authorities," Husayn al-Haidari told Aljazeera by telephone.
Aljazeera has learned that a police station north of Najaf on Saturday came under rocket-propelled grenade attack.
Flames were seen rising from the station.
Clashes between al-Sadr's militia and US-led occupation forces also continued for a second day in the southern city of Kufa, leaving at least one dead and a dozen wounded, including civilians.
No police at mosque
Claims al-Mahdi militiamen were
captured have been proven false
The Iraqi Interior Ministry said on Friday police had entered the Imam Ali mosque and arrested about 400 militiamen.
"The Iraqi police are now in control of the shrine, along with the religious authorities," senior Interior Ministry spokesman Sabah Kadhim had said, one in a series of conflicting statements by various parties on Friday.
However, US military sources denied the ministry's statement. Al-Sadr aide Ahmad al-Shaibani, speaking from inside the site, told Aljazeera the claims were "laughable".
Speculation about who controlled the mosque - revered by Muslims and especially Shia believers - was rife on Friday evening.
Allawi has been under pressure to
end the Najaf crisis peacefully
"The keys of the Imam Ali shrine have been handed over to representatives of the Shia highest religious authority, Ayat Allah Ali al-Sistani," al-Shaibani had said.
However, by late Friday night, al-Shaibani recanted, saying al-Mahdi Army members were still in control of the revered site.
Confusion also seemed to reign in the al-Sistani camp. Representatives of the leading Shia cleric, who is in Britain receiving medical treatment, at first confirmed then denied the handover of the keys.
Al-Shaibani said on Saturday his group was still seeking a peaceful handover to Shia religious authorities, but suggested the al-Mahdi Army stay on as a security force for the site.
Meanwhile, the whereabouts of al-Sadr himself remain unknown.
Interim Prime Minister Iyad Allawi is under severe pressure to end the crisis in Najaf, where al-Sadr's movement has presented a clear challenge to his authority.
But Allawi is reluctant to approve a direct assault on the mosque, which would risk inflaming Muslim opinion against him. There is already some visible damage to the mosque's minarets from recent fighting.
US officials have said their troops will not attack the mosque, although American soldiers, backed by tanks and aircraft, have been active near it.