Over the past two months 3,242 searches of premises have been carried out, 400 people arrested and another 400 placed under house arrest, according to the French Interior Ministry.
Amnesty slammed the measures as "brutal" and said arbitrary night-time searches and house arrests had failed to respect the rights of "hundreds of men, women and children who had been left traumatised and stigmatised".
It said the extended executive powers were often not properly controlled and had produced few concrete results.
Of the 3,242 raids carried out over the past few months only four had resulted in investigations into terror-linked activity with another 21 into alleged promotion of terrorism, the report stated.
Amnesty's workers interviewed 60 people who said the measures had been applied severely, sometimes with excessive force and with little or no explanation.
In certain cases, the report said, the ensuing stigmatisation had led to people losing their jobs.
Toubon's office on Thursday reported that it received 42 requests for help between 26 November and 31 December 2015.
Most of them - 18 - related to raids on homes or properties, while 11 related to house arrests, two of which led to the subjects being fired.
"Collateral damage" included a woman refused access to a school because she was wearing Islamic headcover, workers fired for wearing beards and a refusal to issue a passport.
The ombudsman sounded the alarm about the possibility of a "lasting regime of exception" in an interview with Le Monde newspaper.
"These are not small measures," he told the paper. "They affect freedom of movement, the right to privacy or the right to work or study."
Amnesty called on the French government to suspend the state of emergency, which has also been criticised by the United Nations and the European Council.
But the call is likely to fall on deaf ears.
An overwhelming majority of French people are in favour, according to opinion polls, and the government has indicated it wants to prolong the state of emergency for another three months after it expires on 26 February and introduce the provision for future ones into the constitution.
Parliament will debate the extension after which the Senate will vote on the proposal on 9 February, followed by a vote in the National Assembly on 16 February.
To read our reports of the November 2015 Paris attacks and their aftermath, click here.