Abdulrahman Alhadlaq, the Saudi Arabian interior ministry official, defended the kingdom's record and said that Amnesty's claims "have to be proven".
"Our policies on human rights are very clear and the orders given are for prisoners to be treated with respect and according to international human rights principles," Alhadlaq said.
"If anything happened, it would be an individual case and if it is brought to anybody's attention it will be dealt with."
But Amnesty said more than 3,100 people were being held "in virtual secrecy" and others had been killed in uncertain circumstances.
It criticised the Saudis for carrying out "secret and summary trials" and for reportedly torturing detainees to extract confessions.
"Our policies on human rights are very clear and the orders given are for prisoners to be treated with respect and according to international human rights principles"
Abdulrahman Alhadlaq, Saudi Arabia's interior minister
They said torture methods include "severe beatings with sticks, punching, and suspension from the ceiling, use of electric shocks and sleep deprivation."
"The abuses take place behind a wall of secrecy," Smart said.
"Most [detainees] are held incommunicado for years without trial, and are denied access to lawyers and the courts to challenge the legality of their detention."
Amnesty said it sought Saudi comment on its report but did not receive "any substantive response".
The report came two weeks after the Saudi government said it had convicted 330 al-Qaeda members in the kingdom's first known terrorism trials for suspected members of the network.
One member was sentenced to death, while others were given jail terms, fines and travel bans.
Authorities said the defendants were accused of belonging to the "deviant group," a description often used by Saudi officials for al-Qaeda, as well as a range of other related charges.
The US and other countries strongly pushed Saudi Arabia to crack down on terrorism after it was discovered that 15 of the 19 hijackers in the September 11, 2001 attacks in the United States came from the kingdom.
Amnesty criticised the international community for failing to apply the same pressure on Saudi Arabia to improve its human rights practices for fear of angering a key Middle East ally that is the largest exporter of oil in the world.