The long-running rows have provoked sharp exchanges between the two sides, and while no tangible measures were agreed at the meeting, the mere fact that talks took place was seen as a positive sign.
Violence meanwhile has been rising to levels not seen since 2008 as the Shiite-led government has struggled to head off months of protests by Iraq's Sunni minority, which analysts say has given militant groups fuel and room to manoeuvre on the ground.
"But it is necessary to have a willingness to solve them," Maliki said in a joint news conference with Barzani, with whom he has traded harsh words in recent years.
The Iraqi premier said the Arbil talks would be followed by further visits by both sides.
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Barzani, meanwhile, said the cabinet session marked "an important visit" and described it as a "start for removing all the problems."
Baghdad and Arbil have been deadlocked over several issues for years.
The cabinet session was followed by talks between cabinet ministers and Kurdish regional ministers and a direct meeting between Maliki and Barzani.
It comes just days after the interior ministry in Baghdad issued a strongly-worded statement calling for Kurdish forces to withdraw from disputed territory, threatening a fragile peace between the two sides' militaries.
Maliki's spokesman Ali Mussawi told AFP, that the Arbil meeting would be followed by a cabinet session in the predominantly Sunni Arab western province of Anbar, where anti-government protests have been raging since December.
Iraq's Sunni Arab minority has decried alleged targeting and wrongful arrest by the Shiite-led authorities.