William, the Duke of Cambridge, spoke at Al Noor mosque in the South Island city of Christchurch, one of two mosques where 50 people were killed by a lone gunman during Friday prayers on March 15.
Forty-three people were killed at Al Noor mosque.
"What happened here was fueled by a warped ideology that knows no boundaries," William told an audience that included Prime Minister Jacinda Ardern and other religious and community leaders.
"Extremism in all its forms must be defeated," he said.
William made the two-day visit to New Zealand on behalf of his 93-year-old grandmother Queen Elizabeth, New Zealand's head of state, following a request by Ardern.
Preceded by a large contingent of police and watched by a police helicopter overhead, he was greeted by Ardern and the imam of Al Noor mosque, Gamel Fouda.
He was due to visit the Linwood mosque, where another seven people were killed, later on Friday.
"The message from Christchurch and the message from Al Noor and Linwood mosques could not be more clear. The global ideology of hate will fail to divide us," William said.
Fouda thanked the prince for his speech, saying he had shown "we count."
A 28-year-old man, a suspected white supremacist, has been charged with 50 counts of murder over New Zealand's worst peacetime mass shooting. Another 50 people were wounded in the attacks.
William started his visit on Thursday in Auckland, New Zealand's largest city, where he attended an Anzac Day service in remembrance of Australian and New Zealand war dead.
He later visited the Starship Children's Hospital with Ardern to meet 5-year-old Alen Alsati, who woke recently from a coma after she and her father were wounded in the attack.
Photos and a video posted on Kensington Palace's Twitter account showed William sitting on the side of the child's hospital bed, surrounded by her family and Ardern.
The girl asked if he had a daughter.
"Yes, she's called Charlotte ... she's about the same age as you," William replied.
He flew to Christchurch later on Thursday to meet some of the first responders to the mosque shootings, including ambulance staff."You did an incredible job on a very bad day," he said, according to Kensington Palace's Twitter account.