Justin Welby saw Mohammed bin Salman at Lambeth Palace in London as concern over Saudi Arabia's role in the war in Yemen continued to cause controversy.
Amnesty International UK's director Kate Allen said: "We hope Justin Welby used the meeting as an opportunity to personally communicate the Church's concerns over the thousands of Yemeni civilians killed and injured in reckless and indiscriminate Saudi-led coalition air strikes.
"We also hope the Archbishop was able to express concern over the ongoing jailing of peaceful critics of the Saudi government, including the prisoner of conscience Raif Badawi."
The meeting with the Archbishop came after Prime Minister Theresa May and the Crown Prince used Downing Street talks to lay out plans for a £65 billion trade and investment package.
The Prime Minister also raised the situation in Yemen with the Saudi royal.
The Crown Prince is holding further talks with the PM at Chequers on Thursday, including a private dinner with Mrs May at her official country residence.
Foreign policy issues, including Yemen and Iran, are expected to feature in the talks.
The first day of his visit saw the Crown Prince have an audience with the Queen, and dinner with the Prince of Wales and the Duke of Cambridge.
In a statement following the meeting, Lambeth Palace said the Crown Prince made a strong commitment to promote the flourishing of those of different faith traditions, and to interfaith dialogue within the Kingdom and beyond.
The Crown Prince has been the driving force behind a modernisation programme, Vision 2030, in Saudi Arabia but the reforms have been dismissed as a "mirage" by human rights campaigners.
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