In the letter, headed "Advice for Roma-bound Reds", Manchester United warned that "fans of other English clubs who have made their way independently to the stadium have reported on a number of occasions problems with getting back to the city centre after the game".
"There is a real danger of being attacked by the 'Ultra' fans of AS Roma," the letter continued.
"We realise that fans travelling independently may not wish to give up that independence but we ask you to consider your own safety and welfare as being of paramount importance."
The letter also said fans should "definitely not" go to the Piazza Faminio by metro or use the Nenni Bridge to access the stadium because they are "habitual routes" of the 'Ultras' – a fanatical supporter group of the Italian club, known for their involvement in football-related violence.
Manchester United have claimed that the advice was given because of fears for the safety of their own supporters and was not intended to cause offence to the Italian club.
However, the Rome mayor Walter Veltroni told Italian publication Gazzetta dello Sport that he thought the comments by the Premiership club could create rather than solve problems for the English fans.
"Rome is a serene and welcoming city," he said.
"I consider what appeared on the Manchester United website to be an unfortunate accident, but also dangerous because it risks creating a negative climate."
About 5,000 United fans are thought to be travelling with tickets to see their team play in the Italian capital tonight, although a further 1,000 are expected to turn up empty-handed in the hope of picking up a black market ticket on the night.
Police from the UK are to travel in order to liaise with their European counterparts today and remain in the country until the game has finished and fans have dispersed.
Fears over English fans' safety were raised last year when three Middlesbrough fans were stabbed and nearly a dozen others taken to hospital after clashing with Roma fans when the two teams met in the Uefa Cup in March last year.
Click here to run an energy price comparison, and see if you could be paying less for your gas and electricity.