"To create a safe haven for those terrorists who try to turn Iraqi territory into a base for attacking Iraq's neighbours should be condemned."
Earlier speculation that the conference could herald a thawing of relations between the US and Iran came after earlier sideline talks on the meeting improved relations between Washington and Syria.
US raid criticised
The Iranian foreign minister also criticised the US for continuing to hold five Iranian diplomats who were arrested by US troops at the Iranian liaison office in Irbil, the capital of the northern Iraq's Kurdistan region.
In his speech Mottaki described the detention of the Iranians as a "brazen contravention of international conventions, the breach of Iraq's sovereignty and obvious dishonouring of the Iraqi people and government."
"When the United States arrests five Iranian diplomats in Iraq, it is an act of terrorism."a spokesman for the Iranian delegation at the conference added later.
The US has said the men had links to Iran's elite Revolutionary Guards and that none of them held diplomatic passports.
Lower level talks
Hoshyar Zebari, the Iraqi foreign minister, said that a lower-level meeting between Iranian and US officials had however taken ace on the sidelines of the conference.
"Today, there was a meeting on the sidelines of the conference, at an expert level not a ministerial one, between the American side and the Iranian side," Zebari told a news conference.
Ryan Crocker, US ambassador to Iraq, said he spoke to Abbas Araghchi, Iran's deputy foreign minister, at the Iraq security conference, but played down its significance.
"The exchange, such as it was, was limited and was on Iraq... It was a pass-by meeting," he said.
No breakthrough
Hopes of the highest-level direct talks between Iran and the US since the countries broke diplomatic ties in 1980 first foundered when Mottaki walked out of a dinner attended by Condoleeeza Rice, US secretary of state, on Thursday.
The two officials had exchanged polite conversation at a lunch earlier Thursday, fueling speculation of further talks.
By contrast, Rice met Walid Muallem, Syria's foreign minister, for talks on Thursday, during which she asked him to stop foreign fighters crossing into Iraq to join groups combating US troops and the Shia-led government.
A final statement on Friday's conference meeting on security reaffirmed all participants' desire to "combat terrorist activities and prevent the use of their territory for supplying, organising and launching terrorist operations."
The first day of the conference won Iraq pledges amounting to $30bn in debt relief and an internationally-endorsed roadmap to achieve political and economic stability in five years.
Iraq violence
Meanwhile in Iraq, US-led forces detained 16 suspected fighters on Friday during raids in Baghdad's main Shia district.
The US-led forces were targeting a cell allegedly smuggling a powerful weapon from Iran into Iraq that can pierce armoured vehicles, the military said.
The US military also identified two alleged al-Qaeda aides killed during a US operation this week which targeted Muharib Abdul-Latif al-Jubouri, a senior media officer for the organisation.
They were identified as Sabah Hilal al-Shihawi, an alleged spiritual adviser to al-Jubouri, and Abu Ammar al-Masri, who the US military said was helping with insurgent activity and infrastructure support for al-Qaeda.
Also in Iraq, a roadside bomb blast on Friday killed five Iraqi policemen and wounded two others while they were on a patrol in western Baghdad, police said.
Seven bodies were also found in the Diyala River in Baqouba, 60km northeast of Baghdad, with police saying that snipers prevented medical teams from recovering the remains.