He was referring to US overtures to groups in Anbar and Diyala, encouraging former anti-government fighters to join the fight against al-Qaeda in Iraq.
The US military insists it is not arming groups to fight al-Qaeda in Iraq. Instead, officials say they are re-directing them away from attacks on US troops to confront al-Qaeda in Iraq.
Al-Suneid warned that these armed groups will retain their weapons in the future because of the US overtures.
"We cannot imagine that a neighbourhood is bombed with an excuse that 'we are searching for a terrorist'"
Hassan al-Suneid, adviser to Nuri al-Maliki
He also said US authorities have embarrassed the al-Maliki government through acts such as constructing walls in Baghdad and repeated raids on Sadr City.
Al-Suneid said: "Al-Maliki finds difficulty in understanding [Petraeus] because he moves with a purely American vision, and reality needs a co-ordinated mutual vision."
Al-Maliki's adviser denounced the heavy use of arms by US troops against suspected fighters as human rights violations.
He said US forces use methods that produce results fast, including "building walls, random killings, detentions in ways that are far from human rights and this embarrasses the government in front of its people".
"We cannot imagine that a neighbourhood is bombed with an excuse that 'we are searching for a terrorist,"' he said.