The organisation says its research on the Turkish-Syrian border suggests that around 100 Syrians who often have not registered in Turkey are expelled from Turkey each day.
Advocacy groups are concerned that the deal, which aims to stem the flow of illegal migrants and goes into effect April 4, threatens the rights of asylum seekers, and they question whether Turkey is a safe country for them.
The EU-Turkey deal stipulates the return to Turkey of any Syrian refugee arriving on the Greek islands, to be offset by resettling a Turkey-based Syrian in the EU.
"Having witnessed the creation of Fortress Europe, we are now seeing the copycat construction of Fortress Turkey.
In earlier stages of the conflict, Syrians who held passports were able to cross at regular border gates and even those who entered illegally could register with the authorities. Now only those needing urgent medical care are allowed to enter and there are an estimated 200,000 displaced Syrians within 20 kilometers (12.4 miles) of Turkey's border.
Amnesty also says Turkish of authorities have scaled back the registration of Syrian refugees in the southern provinces which makes it impossible for them to access basic services.
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