After a visit to the kingdom, Ben Emmerson told reporters that a 2014 counter-terrorism law contains an "unacceptably broad definition" of the crime and does not comply with international rights standards.
"I strongly condemn the use of counter-terrorism legislation and penal sanctions against individuals peacefully exercising their rights to freedom of expression", religion, or association, said Emmerson, who reports to the UN's Human Rights Council.
He urged Saudi Arabia to create an independent review mechanism to examine cases of people jailed for exercising such rights "and to commute or pardon all such prisoners with immediate effect".
"I am profoundly concerned" that they remain in detention, he said.
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The list includes Saudi blogger Raif Badawi and human rights lawyer Walid Abulkhair.
Emmerson said he sought to interview people detained for expressing non-violent views but "the government was unable to give access".
The independent expert expressed additional concern about persistent reports of "the use of torture and ill-treatment by law enforcement officials to extract confessions".
Saudi officials denied those and the torture allegations, Emmerson said.
Saudi Arabia is one of the world's most prolific users of the death penalty, including for people convicted of terrorism.
Emmerson said there appear to have been "multiple due process violations" in one death penalty case, "and there may well be others".
At the same time, he said standards of care at the kingdom's prisons for terrorist suspects "are amongst the highest in the world".
Saudi Arabia for more than two years has led a military coalition conducting air strikes in Yemen, where the government says it is battling "state-sponsored terrorists".
Emmerson raised the issue of civilian casualties caused by the coalition in Yemen.
A coalition team of military and legal experts, which it describes as independent, has issued findings on numerous incidents in Yemen.
But Emmerson reminded Saudi Arabia that it has an international legal obligation to conduct a probe "independent of the chain of command" in every case where civilians are reliably believed to have been killed or wounded.