Yassin Majid, the prime minister's spokesman, said on Friday that the two men were in meetings in the Iraqi leader's office in Baghdad's heavily fortified Green Zone. He gave no other details and the US embassy officials were not immediately available for comment.
Negroponte, whose visit was previously unannounced, had served as the American ambassador to Iraq before the current ambassador Zalmay Khalilzad.
"This visit is in the framework of a continuing series of meetings between the Iraqi government and the US administration," Majid said without further elaboration.
The Negroponte visit comes five days after National Security Adviser Stephen Hadley paid an unannounced visit as tensions in the US-Iraqi relations came to the surface after a series of critical statements by al-Maliki.
Hadley met al-Maliki and his security chief, Mouwafak al-Rubaie, telling them he "wanted to reinforce some of the things you have heard from our president".
Al-Rubaie told the AP that Hadley had discussed the work of a five-man committee that al-Maliki and Bush had agreed to establish last week to deal with security issues and speeding the transition to Iraqi control over the country.