UN chief Ban Ki-moon called in Baghdad on Thursday for Iraq and Kuwait to seize a "historic opportunity" to normalise ties, and also said Syria's president must face justice if he uses chemical weapons.

"I believe that a historic opportunity is at hand to fully normalise relations between the two states," Ban said at a news conference with Prime Minister Nuri al-Maliki.

"It is time for both countries to put the past behind and usher in a new era of cooperation," said the UN chief, who also met Foreign Minister Hoshyar Zebari and President Jalal Talabani.

Several outstanding issues between Iraq and Kuwait remain from now-executed president Saddam Hussein's August 1990 invasion of its southern neighbour, including recognition of their border.

Baghdad pays five percent of its oil and gas revenue into a special United Nations fund that pays compensation to Kuwait for its invasion and seven-month occupation of the emirate.

The UN chief, who flew in from Kuwait City, said in the emirate on Wednesday that he is "committed to normalisation and to ensuring Iraq fulfils all of its outstanding international obligations" on Kuwait under UN resolutions.

Ban, who last visited Iraq in March for an Arab summit, said his talks in Baghdad also covered the current political impasse in Baghdad, tensions between it and the Kurdish regional government and the conflict in Syria.

He said President Bashar al-Assad should be "brought to justice" if his regime uses chemical weapons to combat the armed revolt in Syria.

"I have expressed my gravest concerns to (the) government of Syria and I have sent a letter directed to President Assad a couple of days ago," Ban said.

"I have warned that in any case, if chemical weapons is used, then whoever (it) may be will have to be brought to justice, and it will create serious consequences to those people."

The Damascus government, fighting to prevent the capital from falling to rebel forces, has insisted it would never resort to chemical weapons.

But Washington fears battlefield advances by rebels could prompt Assad to use chemical arms, or that such stocks could become insecure or find their way into the hands of groups hostile to the United States and its allies.

US Under Secretary of Defence James Miller told reporters in Baghdad on Thursday that the use of chemical weapons in Syria is a "red line" for Washington, and that "we also wish to emphasise the importance that... the Bashar al-Assad regime control and not employ its chemical weapons."

Ban, meanwhile, urged the Iraqi government to keep its borders open to Syrian refugees fleeing the conflict.

"The secretary general... urged Iraq to continue to be generous and keep its borders open to enable Syrian refugees and Iraqi returnees to seek safety in Iraq," a statement said.

Hundreds of thousands of Iraqis fled to Syria to escape the violence in their homeland that peaked in 2006-2007 but have now found themselves caught up in the intensifying conflict raging in the neighbouring country.

Ban's visit also came amid tensions between Iraq's federal government and the autonomous Kurdistan region, in which Baghdad has sent troop reinforcements to disputed areas of the north.

"I also expressed hope that divergences over disputed territories in northern Iraq can be resolved. There is no alternative to peaceful coexistence within a united federal Iraq," the UN chief said.

Talks between federal and Kurdish security officials broke down last week over Baghdad's refusal to scrap a new federal military command that covers disputed territory, according to the Iraqi Kurds.

The dispute over territory in northern Iraq is the greatest threat to the country's long-term stability, diplomats say.