Turkish authorities in several cities, including Istanbul, have stopped registering new asylum seekers fleeing Syria, according to Human Rights Watch.
The suspension in new registrations means that some Syrian refugees have had to return to Syria, are unlawfully deported, or have been denied health care and education.
The rights group said that provinces had stopped registering asylum to deter them from seeking refuge in Turkey.
The report was based on insider information from local Turkish groups working with refugees and former government officials, as well as interviews with Syrian refugees.
Europe turning a blind eye
Gerry Simpson, associate refugee programme director at HRW, said Europe was "turning a blind eye to Turkey."
"Forcing Syrians who manage to get past Turkey's border guards to live in legal limbo only risks driving them underground and onward to the EU," he added.
This latest development comes as the European Union prepares to release the second batch of $3 billion under its March migration deal. The EU maintains that under the deal, Turkey is a safe country to return Syrian asylum seekers.
But Syrians who spoke to HRW said that Turkish police were deporting them in groups of up to 20 for not having a permit, adding that hospitals and schools had refused to take them without the paperwork.
A permit protects Syrians from arrest and deportation back to Syria.
Turkey's bid to return Syrian refugees
In February, Turkish President Recep Tayyip Erdogan vowed to return millions of Syrian refugees to their homes during an address to local provincial leaders.
The Turkish president said: "we want our refugee brothers and sisters to return to their land, to their homes. We are not in a position to hide 3.5 million here forever."
Since the outbreak of the Syrian civil war in 2011, Turkey has become host to the world's biggest refugee population, taking in approximately 3.6 millions Syrians.