President Hamid Karzai has said those opposed to Afghanistan's close links with Washington are to blame for riots in which at least 15 people have died.
Burning the US flag - protesters vent their frustration
He said protesters were "against the strengthening of the peace process".
But Mr Karzai also said US military actions had helped create a mood of resentment among Afghan people which had contributed to the violence.
Afghan unrest has spread following claims that US guards at Guantanamo Bay desecrated copies of the Koran.
More protests broke out on Saturday in the northern Afghan province of Baghlan, local officials told the BBC.
Newsweek magazine reported on 9 May that interrogators at the Guantanamo Bay detention camp placed Korans on toilets to upset suspects, and in one case "flushed a holy book down the toilet".
In Baghlan, officials said hundreds of demonstrators took to the streets.
They said five people had been arrested and that explosive materials were also seized.
In the province's Band-e-Ghouri district demonstrators burned an effigy of President George Bush calling on the US to make an apology over the incident.
The demonstrators went on to temporarily block the highway between cities of Mazar-i-Sharif and Plikhumary.
There were also unconfirmed reports on Saturday of demonstrations in the southern town of Spin Boldak, in neighbouring Zabul province and in Farah province in the west.
"Those people demonstrating are against the strategic partnership of Afghanistan with the international community, especially the United States," President Karzai told correspondents at his palace in Kabul.
"They want us to have a bad name in the international community."
Mr Karzai, who has just returned from Brussels, said his mission to Europe to press for continued international aid was made much harder as a result of the riots.
Some Europeans had asked why they should help when Afghans were only destroying things, he said.
The president said investigations were taking to place to determine who was behind the demonstrations, amid claims that militant groups and outsiders were helping to stoke them.
But when asked if anger over sometimes heavy-handed US military tactics had helped fuel the trouble, he said there had been mistakes by American forces and that his government was taking steps to exert greater control over their operations.
Mr Karzai said his government was close to agreement with the US on taking control of all Afghan prisoners currently detained in US military jails in Afghanistan.
But he stressed that the country still depended on international support and without it Afghanistan would return to chaos.
Chief Justice Fazl Hadi Shinwari on Saturday said the US should be ready to apologise if the allegations over the Koran desecrations prove to be true.
"If the Americans have done this, then they should admit it and punish those who did it and apologise to Muslims," he said.
Insulting the Koran or the Prophet Muhammad is regarded as blasphemy and punishable by death in Afghanistan.
On Friday, US Secretary of State Condoleezza Rice appealed to Muslims to resist calls for violence, and promised that her country was investigating the allegations.
Ms Rice said on Thursday that desecration was abhorrent and disrespect for the Koran would not be tolerated.
The US is holding about 520 inmates at Guantanamo Bay, many of them al-Qaeda and Taleban suspects captured in Pakistan and Afghanistan following the 11 September 2001 attacks in the US and subsequent US-led invasion of Afghanistan.