The soldiers based near al-Suwayra left Iraq and are expected to return to Ukraine by Tuesday, the ministry said.
Earlier this month, President Viktor Yushchenko and top defence officials ordered a phased withdrawal of Ukraine's 1650-strong contingent from the US coalition in Iraq.
Ukraine has lost 17 soldiers in Iraq, and the deployment is deeply unpopular among people in the former Soviet republic.
Ukraine plans to withdraw about 590 soldiers from Iraq by May and the rest by October, the Defence Ministry said.
Yushchenko said on 1 March that the pullout would be completed by 15 October, but Defence Minister Anatoly Gritsenko later said Ukraine might leave some troops in Iraq two months beyond that deadline.
Ukraine strongly opposed the US-led war but later agreed to send a large contingent to serve under Polish command in central and southern Iraq.
The move was widely seen as an effort by former President Leonid Kuchma to repair relations with Washington, frayed by allegations that he had approved the sale of radar systems and other military equipment to Saddam Hussein's government.
Yushchenko said the pullout
would be completed in October
Meeting Ukrainian Foreign Minister Borys Tarasyuk on Friday, US Secretary of State Condoleezza Rice on Friday hailed the "special relations" between the United States and Ukraine - where the Western-oriented Yushchenko took office in January - and brushed aside concerns about the planned withdrawal.
US supplies targeted
A roadside bomb exploded at about 8am on Saturday as a convoy carrying supplies for the US military passed through Makhul, close to the northern oil refinery town of Baiji, 220km north of Baghdad, killing one of the drivers, said police Lieutenant Colonel Hasan Salah.
"The driver might be Turkish because the truck had Turkish plates," he said.
Most Turkish drivers have stopped venturing out on the roads linking Baghdad to the northern city of Mosul after a series of attacks targeting supplies for US forces in the area over the past year.
Iraqi drivers are doing the job now.
In Baiji, a dawn mortar attack on an Iraqi army barracks wounded one soldier and destroyed a vehicle, said Captain Hasan Yusuf.
In Ishaki, farther south, a mortar attack partly destroyed an abandoned building of a joint Iraqi-US security task force, said police.
In nearby Balad, fighting raged for about two hours starting at 8pm on Friday after some fighters were ambushed in the al-Nabai area, said Lieutenant Husain Abbas.
Three soldiers were wounded and a car belonging to the attackers was destroyed and left burning at the scene, Abbas added.
In Samarra, commandos from the Interior Ministry set up checkpoints at the main entrances and continued their raids and arrests of fighters in the area.
Iraqi police in the northern city of Mosul said on Saturday that three police officers were shot dead and another was wounded at a funeral procession.
The attack occurred as police were taking part in a procession held for a colleague's wife and two children who died in a roadside bomb attack in Mosul a day earlier, said policeman Ammar Husain.
Meanwhile, the United Iraqi Alliance and Kurdish parties agreed on the makeup of the three-member Presidency Council to be chosen by Iraq's parliament.
It would include Jalal Talabani as Iraq's first Kurdish president and a Sunni Arab and a Shia Arab for the two vice-presidents, said Ali al-Dabagh, a negotiator for the Shia alliance.
Names were not announced for those jobs.