Before the visit, Maliki told Egyptian newspaper editors "those who are infiltrating Iraq are coming from our neighbours ... and bringing private agendas, or agendas from the countries they are coming from", according to a statement from his office.
On Monday, General Ray Odierno, the senior US commander in Iraq, said that although the "flow of foreign fighters in Iraq has decreased significantly ... we're still a little bit concerned with Syria's role in this".
But Thabet Salem, a journalist and political commentator in Damascus, told Al Jazeera that the Syrians had "submitted proof" that they had done everything possible to stop foreign fighters crossing into Iraq.
"They have deployed 14,752 soldiers alongside the borders, 500 or more posts are observing the borders, while the Iraq have done absolutely nothing, along with the Americans, on their side of the borders," he said.
"The Syrians will exploit the visit to tell Maliki 'please stop doing these allegations, you have to do something, we have done what we can'."
Maliki arrived a week after a US military delegation visiting Damascus reportedly discussed Iraqi security with Syrian officials, which Baghdad criticised for taking place without Iraqi representation.
Oil and water
The Iraqi prime minister was accompanied on his visit by Hussein al-Shahristani, the Iraqi oil minister, and Latif Rashid, the water minister, as well as senior security officials.
Syrian and Iraqi oil officials are likely to discuss a plan to reopen a closed oil pipeline from Iraq's northern oilfields to Syria's Mediterranean coast.
During talks with Mailiki in Baghdad in April, Mohammed Naji Otri, the Syrian prime minister, agreed to repair the pipeline, which was shut off following the US-led invasion of Iraq in 2003.
Before March 2003, Syria received around 200,000 barrels of oil a day from Iraq at preferential prices, enabling it to profit from sales on the international market.
Water is also a major issue for the two neighbours, with Baghdad frequently complaining that the flow of the Euphrates river is not sufficent to meet Iraq's agricultural needs.
In July, Baghdad called for talks with Ankara and Damascus over the issue.