A statement Monday from the organization, based in London, said new guidelines instruct Israeli officials to inform detainees seeking asylum they face years in detention if they chose not to return home.
The organization said pressure is being put on at least 1,400 asylum seekers from Eritrea and Sudan, some of whom have been detained for more than a year.
The statement cited 14 Eritreans who left Israel for Eritrea this month, some of whom told the United Nations' refugee agency they would "do anything to get out of prison."
"This is using the threat of prolonged detention to force Eritrean and Sudanese nationals to give up their asylum claims. Israel should end its unlawful detention policy and release all asylum seekers while their claims are fairly examined," said Gerry Simpson, a Human Rights Watch senior refugee researcher.