Spokesman Ali al-Dabbagh said the military action was a violation of Iraqi sovereignty, and he called on the Turkish government to engage the Iraqis in dialogue instead.
"The Iraqi Cabinet has denounced the Turkish army's incursion," al-Dabbagh said in a televised statement after the government met to discuss the issue. "The Cabinet calls on Turkey to withdraw its troops immediately and stop military interference."
Turkey launched the incursion into northern Iraq on Thursday against separatist rebels from the Kurdistan Workers' Party, or PKK. The PKK wants autonomy for the predominantly Kurdish southeastern Turkey and rebels have carried out attacks in Turkey from bases in Kurdish Iraq. The conflict started in 1984 and has killed up to 40,000 people.
Turkey has assured the Iraqi government and the U.S. military that the operation would be limited to attacks on rebels. The U.S. and European Union consider the PKK a terrorist group.
Al-Dabbagh acknowledged the threat to Turkey posed by the rebels and said Iraq stood ready to work through trilateral discussions with the United States or any bilateral dialogue to prevent the PKK from using Iraqi territory to attack Turkey.
But, he said, "unilateral military activity is an unacceptable deed and endangers the good bilateral relations between our two neighboring countries."
Al-Dabbagh added that Iraq understood Turkey's concerns and that the government would "not allow Iraqi lands to be used as a base from which operations are launched to destabilize security in the region."
The Turkish military has said 153 rebels have been killed in the operation. The Kurdish rebels disputed the claim and warned that Turkey had entered a conflict that it cannot win.
A statement posted on the military's Web site Monday also said two more soldiers were killed in fighting, but gave no details. The deaths would bring the total Turkish military fatalities since the start of the incursion Thursday to 17.
Meanwhile, processions of black-clad men flagellating themselves with chains to express grief at the martyrdom of a revered Shiite figure marched Tuesday through the city of Karbala, as a national pilgrimage marred by deadly attacks neared its conclusion.
Shiites from all over Iraq have walked to Karbala, 50 miles south of Baghdad for Arbaeen. The commemoration marks the end the mourning period following the anniversary of the death of Imam Hussein, who was slain in a seventh century battle and is buried in Karbala, along with his half brother Imam Abbas.
Police Chief Raid Shakir Jawdat has said 40,000 police officers and military troops are being deployed to prevent attacks, with patrols on the outskirts of the city guarding against rocket or mortar attacks and hundreds of snipers on tall buildings.
The United States blamed Sunni-led al Qaeda in Iraq on Monday for the sectarian attacks, the worst of which killed 56 and wounded scores of pilgrims who were taking a break from their travels Sunday at a refreshment tent.
U.S. Embassy spokesman Philip Reeker said that while al Qaeda in Iraq has been "severely damaged," it remains a "dangerous threat."