The human rights group published a statement on Tuesday saying the health of the hunger strikers was deteriorating.
It called on the authorities to ensure that they receive appropriate medical care and have regular access to independent doctors.
Amnesty's statement comes after Malaysia's own state-backed Human Rights Commission pressed for the men to be accused of a crime or set free.
The detainees include Nik Adli, the son of the opposition Islamic Party (PAS) spiritual leader Nik Aziz Nik Mat. All 16 have been held on suspicion of having terrorist links since 2001.
"Presumed guilty of unspecified links to 'terrorism' and denied the right to defend themselves before the courts, Malaysia's 'forgotten' prisoners continue to endure prolonged detention," Amnesty said.
"Detention without trial remains a violation of human rights - whether in Malaysia's Kamunting Detention Camp or in Guantanamo Bay."
A total of more than 80 alleged "terrorists" are held under Malaysia's Internal Security Act (ISA), which allows for two-year detention periods that can be renewed indefinitely.
Rights groups have urged the government to scrap the legislation, but it maintains that detention without trial is needed as a first line of defence.
Amnesty said the law "has frequently been deployed by the authorities in a politically-motivated and selective manner" since it was introduced to fight a communist insurgency in the 1960s.
"Detention without trial remains a violation of human rights - whether in Malaysia's Kamunting Detention Camp or in Guantanamo Bay"
Amnesty International statement
Several of the detainees are members of PAS, which presents the main challenge to the government of PM Abd Allah Ahmad Badawi in elections due on 21 March.
Pressed last week about the fate of the detainees, Abd Allah did not address the issue of the hunger strike directly, but said: "all these cases are reviewed very regularly.
"So it is not something we do for the pleasure of doing it. There must be some reasons."