He returned to the capital Tegucigalpa this week and has been holed up in the Brazilian embassy, outside which about 4,000 of his supporters gathered Tuesday before being dispersed by police using truncheons and tear gas.
"The situation in Honduras can only be described as alarming," said Susan Lee, Amnesty's Americas director.
Amnesty said it had documented a sharp rise in police beatings, mass arrests and harassment of activists since Zelaya was forced out of office.
"The attacks against human rights defenders, suspension of news outlets, beating of demonstrators by the police and ever increasing reports of mass arrests indicate that human rights and the rule of law in Honduras are at grave risk," Lee said.
She urged the Honduran authorities to "stop the policy of repression and violence and instead respect the rights of freedom of expression and association".
"We also urge the international community to urgently seek a solution, before Honduras sinks even deeper into a human rights crisis," she said.
Zelaya appealed to the UN General Assembly meeting in New York on Wednesday "not to abandon the Honduran people at this critical time".
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