During a visit to the region yesterday he told people in Cottingley, near Bradford, he understood their "anger, resentment and bewilderment" after vandals last year destroyed a statue of Christ on the war memorial at St Michael and All Angels Church.
But he said: "The crucial issue, it seems to me, is how you deal with the whole question of alienation.
"How do we tackle the issue of young people left shallow rooted and bereft of a spiritual and moral dimension in their lives?
"These, of course, are questions which I am sure as a community you are facing."
In glorious sunshine in front of the new memorial to the 29 men from the parish who died between 1914 and 1918, the Prince said the hardest part of being a Christian was to "love your neighbour and do good to those who hate you".
Speaking after attending a thanksgiving service for the new memorial, led by the Rev Sue Pennington, he said: "I do hope that it will remind all of us of the importance of reconnecting all of us to our roots and remembering that it is so important to have that thread of continuity that links one generation with another."
He then spent half an hour chatting to crowds of well-wishers who turned out to greet him, before meeting members of local community groups to discuss their plans for the regeneration of the area.
People from the parish are hoping to work with the Prince's Trust to launch a £500,000 fundraising drive to rebuild the church, a 1960s building which has fallen into disrepair.
Earlier in the day, arriving by Royal train at Bradford Forster Square station, the Prince visited the Inland Revenue headquarters and met 22 representatives of the business community to discuss how businesses have contributed to the local community and what they could offer youth development in the city.
Unveiling a plaque to mark his visit he praised the Inland Revenue's work, saying it made a profound difference to small organisations and charities and the battle against red tape and bureaucracy.
Slightly behind schedule, he was then driven to Meanwood Valley Urban Farm, Leeds, where he was greeted with a barrage of cheers by pupils from Potternewton and Miles Hill primary schools waving Union flags and banners they had made.
Wearing a grey pinstripe suit and a red rose in his lapel, he chatted to the children asking them whether they had seen the pigs at the farm and whether they grew vegetables themselves.
Danielle Cawley and Stefanie Sword, both 10, of Potternewton Primary School, said they had been preparing for weeks at school to meet the prince. Danielle said: "He was very polite when he spoke to us. It was all worth the wait."
The Prince, who is patron of the Federation of City Farms and Community Gardens, then toured the farm observing traditional skills such as wool carding, gardening, plus he saw a Gloucester Old Spot sow and her litter of seven piglets.
He was presented with organic vegetables, honey from the farm's four hives of 200,000 bees, a bat-box made by schoolchildren and a broom constructed from heather.
One special moment came for Ju Juinn Law a pupil at Grafton School, Woodhouse, Leeds when she flung her arms around the Prince as he was inspecting the brooms.
The Prince paid tribute to the hard work that has gone into running the farm which was established in 1980 and was one of the first city farms in the country.
"The real importance of these city farms is to enable people to remain in connection with the soil and with growing things. Unless people experience working with animals and plants it is very difficult to get the message through," he said.