The Pope has pressured George W Bush over what he called recent "deplorable events" in Iraq, as anti-war protesters set off flares in the Italian capital.
The Pope has criticised the US-led war in Iraq
The Pope described the situation in the Middle East as one of "grave unrest".
Mr Bush held talks with the Pope at the start of a three-day visit to Europe to attend World War II commemorations.
The US president is also meeting Italian Prime Minister Silvio Berlusconi who, unlike the Pope, has been a firm supporter of the Iraq war.
Mr Berlusconi is among Mr Bush's closest European allies.
Despite the opposition of most people in Italy to the war in Iraq, he has repeatedly pledged he will keep Italian troops in Iraq and rejected suggestions that they might leave early.
Thousands of police have been deployed in Rome amid fears that the demonstrations in Rome could turn violent.
Resolution 'more difficult'
In his meeting at the Vatican, Mr Bush presented the Pope with the American Medal of Freedom, calling him a "son of Poland who became the Bishop of Rome and a hero of our time".
The Pope, who has Parkinson's Disease, struggled to speak clearly as he addressed the US president.
He reiterated the Vatican's opposition to the war in Iraq and said everyone wanted the situation to be normalised as quickly as possible "with the active participation of the international community and in particular the United Nations".
He added: "In the past few weeks other deplorable events have come to light which have troubled the civic and religious conscience of all, and made more difficult a serene and resolute commitment to shared human values: in the absence of such a commitment neither war nor terrorism will ever be overcome."
The Pope did, however, praise Mr Bush's "commitment to the promotion of moral values in American society, particularly with regard to respect for life and the family".
Mr Bush will later lay a wreath at a memorial to victims of a massacre by Nazis several miles away at the Ardeatine Caves, or Fosse Ardeatine.
As security forces cordoned off entire areas of Rome in preparation for the visit, Mr Berlusconi said he was worried about violence and called on protesters to show "maturity and understanding of history".
Small groups of protesters, some carrying the rainbow-coloured flags that have become the symbol of the anti-war movement in Italy, gathered in the capital late morning.
In isolated incidents, they set fire to overturned rubbish bins and threw fireworks at government buildings.
Thousands travelling to the march by bus and train from across Italy were expected to arrive in Rome by late afternoon.
Mr Bush will spend two days in the Italian capital before travelling to France for D-Day commemorations.
The BBC's Clive Myrie, who is travelling with the US president, says this is an important trip to Europe for Mr Bush - an opportunity to push for a new UN resolution on Iraq with some key Nato allies face to face.
But recent images of Italian hostages being held in Iraq have reinforced opposition to the war among many Italians, our correspondent says.
The US state department has warned Americans in Italy of the "potential for violence" and to avoid areas in which crowds are expected to gather.
Timetable of events 6 June
0900 Franco-American ceremony begins at the US cemetery in Colleville
1100 Bi-national service at British Cemetery Bayeux
1430 International march past on cliff top Arromanches
1730 French national ceremony in Ouistream
1730 British veterans march in Arromanches
1820 French German ceremony in Caen
All timings are local
Rome police chief Achille Serra said he had not had any indications of the possibility of terrorist attacks targeting the visit, but there were "signs of a difficult situation regarding public order".
"If there is violence, it will be violence for violence sake," he said.
"When the world is so mixed and especially when protesters are planning to demonstrate in so many different locations in the city, it becomes difficult to predict."
Mr Bush is later to fly to France for D-Day ceremonies.
A huge security operation is also in place there, with 30,000 police and security forces mobilised, including a 12,000-strong contingent of the French army.
Up to 100,000 visitors are expected in the Normandy region for the D-Day anniversary ceremonies, including world dignitaries, thousands of veterans and representatives from the media.