They criticised a public campaign launched by the Hungarian government this month that they said portrayed refugees, most of them coming from war-torn Syria, as "criminals, invaders and terrorists based on their religious beliefs and places of origin".
The campaign has seen full-page messages in national newspapers appear with the headline: "The quota increases the terror threat!" against a black background.
It refers to EU plans to distribute 160,000 refugees and migrants across the bloc, with Slovakia and Hungary due to take in around 2,300 people each.
Other messages read: "An illegal immigrant arrives in Europe on average every 12 seconds"; "We don`t know who they are, or what their intentions are" and "We don`t know how many hidden terrorists are among them".
Hungary has taken a hardline stance on the refugee crisis, sealing off its southern borders with a barbed wire fence to stop the influx of migrants.
Hungary`s Foreign Minister Peter Szijjarto reacted to the criticism, denying that the country was trying to sow fear of refugees and migrants, according to the Hungarian news agency MTI.
"Hungary is talking about reality... it offers, as before, protection to those who really need it, but it cannot welcome tens or hundreds of thousands of economic migrants," the agency quoted him as saying.
"Furthermore we have never claimed that all migrants were terrorists, but with the uncontrolled flow of migrants, the terrorist threat grows in Europe," he added.
The rights organisations said that Hungary needs to contribute to resolving the crisis and "acknowledge that refugees are coming to Europe, after having endured trauma, tragedy and loss... to start a new life far from the upheavals of war and conflict."
Since January nearly 970,000 refugees and migrants have flooded Europe, with most of them passing through Greece and its Aegean islands, according to UNHCR.
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