In a 65-page report, the human rights organisation said an unknown number of detained people have been held in secret without access to lawyers or visitors for months or years while those brought to trial often face grossly unfair procedures.
"The scale of human rights violations is shocking. Thousands of people have had their lives turned upside down or destroyed by violations of their rights in the name of countering terrorism," Amnesty suggested in the detailed report.
An unknown number of human rights defenders, advocates of political reform and members of religious minorities who had committed no crime recognised in international law had been caught in a "security-related repression", it wrote.
A spokesman for the interior ministry in Riyadh had no immediate comment on the report, which highlighted several cases of people whom Amnesty said had been detained under questionable circumstances.
Saudi Arabia is an absolute monarchy without an elected parliament whose courts are run by clerics applying an austere version of mainstream Sunni Islam.
The report was published after Saudi Arabia handed out verdicts earlier this month in the first publicly reported trials since al-Qaeda-linked militants began a campaign in 2003 to destabilise the world's biggest oil exporter.
In total 289 Saudis and 41 foreigners received sentences of up to 30 years in prison, state media said last week, without disclosing the nationalities. One unnamed person was sentenced to death, a government official has told Reuters.
A group called al-Qaeda in the Arabian Peninsula began a campaign to destabilise the government in 2003 but violence was ended by security forces in co-operation with foreign experts. The last major attack was in 2006.
Local human right activists have long accused Saudi Arabia of using counter-terrorism efforts to detain opposition activists demanding democratic reforms or refusing to provide figures of detained and arrested people.
The United States, which is Saudi Arabia's main ally, and other Western countries rarely criticise the Gulf Arab state, which controls more than a fifth of global crude reserves and is a major holder of dollar assets as well as a key trading nation.
King Abdullah has tried some reforms since taking office in 2005 and removed two hardline clerics from top positions in a cabinet reshuffle in February aimed at curbing the influence of the religious establishment in education and judiciary.
But diplomats and analysts say his room for manoeuvre is limited given the resistance of conservatives in the ruling family.
Amnesty criticises Saudi Arabia's 'shocking' human rights violations - Telegraph
