The government is pursuing "harmful policies focused on deterring and containing asylum seekers and refugees," 45 NGOs and civil society groups said in a report.
They urged the European Union and Greek government to abandon plans to restrict the movement of people in the refugee camps.
The European Commission is providing financial and technical support to Greece to construct walls around dozens of existing camps and to build closed camps in remote locations on the Aegean islands, the report said.
European home affairs commissioner Yvla Johansson last March announced 276 million euros ($330 million) of EU funding to build migrant centres on five Aegean islands facing Turkey, including Lesbos.
As numbers ballooned to 20,000 at Moria, Europe's biggest camp, became a byword for squalor and violence.
The camp burnt down last September 9. No one died in the blaze, but it sparked a chaotic exodus of 12,000 asylum seekers.
A new camp was due to open on Lesbos before winter, but work has yet to begin. On Samos island a new camp is due to open at the end of the month.
The report said the new structures "will impede effective identification and protection of vulnerable people, limit access to services and assistance for asylum seekers, and exacerbate the harmful effects of displacement and containment on individuals' mental health."
The International Rescue Committee (IRC) said 96 percent of refugees it treats on Lesbos are depressed and 93 percent suffer from acute anxiety.
Dukas Protogiros, IRC psychologist on the island, said the plans would "simply exacerbate the mental health crisis already experienced by so many people trapped on the islands."
Athens boasts of bringing order to chaos by having tackled critical overcrowding in the camps.
Only 3,752 migrants remain on Lesbos today, compared with 13,000 a year ago, according to official statistics.
"We managed to regain control," said migration minister Notis Mitarachi.
"We reduced flows, we reduced residents, we minimised the impact on local communities. We have turned an uncontrollable crisis into a manageable situation."
Rights groups attribute the reduction in numbers to a policy of forcibly pushing arrivals back to Turkey.
The conservative Greek government denies such claims.
