The pope told Bush on Friday his visit to Europe comes "at a moment of great concern for the continuing situation of grave unrest in the Middle East, both in Iraq and the Holy Land".
"It is the evident desire of everyone that this situation now be normalised as quickly as possible with the active participation of the international community and, in particular, the United Nations Organisation, in order to ensure a speedy return of Iraq's sovereignty, in conditions of security for all its people."
John Paul II has been one of the staunchest critics of Bush's decision to go to war in Iraq.
The pope also made a veiled reference to recent revelations of the abuse of Iraqi prisoners by US troops in Iraq.
"In the past few weeks other deplorable events have come to light which have troubled the civil and religious conscience of all, and made more difficult a serene and resolute commitment to shared human values."
He said that in the absence of such a commitment, "neither war nor terrorism will ever be overcome".
Bush, who described John Paul II as "a devoted servant of God who has championed the cause of the poor", presented the 84-year-old head of the Roman Catholic Church with the Presidential Medal of Freedom, his country's highest civilian award.
Earlier on Friday, police turned Rome into a fortress as anti-war protesters had pledged to give Bush a heated reception during his 36-hour visit.
Carabinieri police saturated the historic city centre, with heavy concentrations of the paramilitary force along the main thoroughfares and piazzas, as well as at bridges, rail stations and airports. Helicopters droned overhead.
Bush presented the Pope with
the Presidential Medal of Freedom
The interior ministry has mobilised some 10,000 security forces. Traffic in the city centre was notably lighter than normal as many residents stayed away from possible flashpoints. The US State Department on Thursday issued a warning to American citizens living in Italy to avoid crowds.
Protesters were on the streets from early morning, but the main demonstration organised by the Communists and Greens was scheduled for mid-afternoon in central Rome.
"We're here to tell Bush he's really not welcome, but we want to say it with a peaceful demonstration," a youth with a megaphone said as the first marchers, many waving multicoloured peace flags, took to the streets in eastern Rome.
Closer to the centre, a group of young people set tyres ablaze on a bridge over the Tiber river.
Around 1000 demonstrators arrived in Rome by train from Milan to join the street protests, rail authorities said.
Many office and apartment windows in the city centre have been draped with the rainbow-coloured peace flags in a polite message to Bush over his Iraq policy, which is supported by Italian Pime Minister Silvio Berlusconi.
The main centre-left opposition parties, who oppose the visit,
said however they would not take part in demonstrations out of respect for the US soldiers who died in the liberation of Rome, the commemoration of which is the official reason for the president's visit.
He was due to attend a wreath-laying ceremony in the afternoon at the Ardeatine Caves outside Rome, the site of one of Italy's worst massacres of civilians at the hands of the Nazis.
Prime Minister Berlusconi has
strong backed Bush's Iraq policy
Bush and his wife Laura, who arrived at Rome's Ciampino airport shortly after midnight, spent the night at the US ambassador Mel Sembler's heavily guarded residence in the leafy Parioli suburb of the city. Nearby roads were closed to traffic.