Prince Khaled al-Faisal was speaking at a news conference to discuss the annual hajj pilgrimage, which ends on Thursday and has added to tensions between Riyadh and Tehran.
"I call on Muslim leaders, whether they are political leaders, ulemas (scholars), or intellectuals, to combat sectarianism," Faisal said.
For the first time in nearly three decades, Iran's 64,000 pilgrims are not attending the hajj in Sunni-dominated Saudi Arabia after the two regional rivals failed to agree on security and logistics.
Saudi Arabia is home to Islam's holiest sites, which pilgrims visit during the hajj, and is the seat of Sunni Islam which predominates in the Muslim world.
The kingdom is founded on the teachings of 18th century Sunni preacher Sheikh Mohammed bin Abdul Wahhab, whose ideas have themselves been decried by critics as a driving force behind sectarianism and an inspiration to violent jihadists.
Iran is the world's major Shiite power, and the two nations are at odds over a number of regional issues including the wars in Syria and Yemen.
"Islam is unique. There is no multiple Islam," said Faisal, president of the Central Hajj Committee.
He said this year's hajj occurred without incident despite "the lies and allegations... Of those who wanted to place in doubt the capacity of the kingdom to serve the pilgrims."
Among its concerns over Iranian participation in this year's hajj, Riyadh said Tehran had demanded the right to organise demonstrations.
Tehran in turn accused Riyadh of "blocking the path leading to Allah".
Security was one of the contentious issues following last year's hajj stampede which, according to foreign officials, killed roughly 2,300 people.
Just days before the hajj began on Saturday Iran's supreme leader Ayatollah Ali Khamenei questioned Saudi Arabia's right to manage Islam's holiest sites.
He called the Saudi ruling family "puny Satans" who had politicised the pilgrimage. Khamenei also said Saudi authorities "murdered" the stampede victims.
Saudi Arabia's Grand Mufti Abdulaziz al-Sheikh retaliated by telling a newspaper that Iranians "are not Muslims".
Reiterating a point made on Tuesday by King Salman, Faisal said Saudi Arabia does not interfere in Iran's internal affairs "but we don't permit the holy sites and the hajj to be used for political ends".
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