The rights watchdog said last Saturday's decision against 72 people had treated peaceful activists in the same way as Bahrainis suspected of travelling to Iraq or Syria to fight for the Islamic State jihadist group.
"The authorities have put the names of a number of known Bahraini human rights and political activists on the same list as other Bahrainis who have been alleged IS fighters," it said.
Amnesty said any move that risked leaving a person stateless should be taken only after due legal process and within the strict limits set by international conventions.
"Bahraini journalists who dare to express critical views already face serious risks, including legal action and imprisonment. Now Bahrain is punishing them by taking away what they value most," it said.
Information Minister Isa Abdulrahman al-Hammadi has said most of those targeted "are abroad and can challenge the decision legally".
The Sunni-ruled but Shiite-majority Gulf state has been wracked by unrest since security forces crushed Shiite-led protests for a parliamentary government and a constitutional monarchy in 2011.
One of them, Farhad Khorshid Afrah is being held by authorities after his arrest at Bahrain's international airport upon his return home from Iran, it said.
Al-Wefaq said he had been stripped of his nationality while on pilgrimage to Shiite holy sites in Iraq along with his wife and two daughters.
It is not the first time that Bahrain has used counter-terrorism powers to strip dissidents of their citizenship but last week's decision targeted the largest number so far.