Thousands of Syrian refugees have been illegally returned to their homeland over the past few months, exposing "fatal flaws" in the refugee deal signed between Turkey and the EU in March, Amnesty International has warned.

An estimated 100 men, women and children have been sent back to Syria almost every day since mid-January, Amnesty said today. Those sent back include children as young as nine and a woman who was eight months pregnant. It described the practice – illegal under international law – as an "open secret" in the region.

Under the latest EU deal, Turkey agreed that it will take back all migrants and refugees who crossed illegally into Greece in exchange for financial aid, faster visa-free travel for Turks and slightly accelerated EU membership talks. European countries have pledged to accept one refugee directly from camps in Turkey in return for every person shipped back.

Turkey has taken in around 2.7 million refugees from Syria since the civil war began in 2011.

However, the legality of the deal hinges on Turkey being a "safe third country" of asylum – an understanding that has been thrown into doubt by Amnesty's allegations. The Syrian Observatory for Human Rights, a UK-based monitoring group, also this week warned that at least 16 refugees have been shot dead by Turkish border forces in the last four months.

Turkey's foreign ministry denied Syrians were being sent back against their will, while a spokesman for the European Commission said it took the allegations seriously and would raise them with Ankara.

Separately, the UN refugee agency UNHCR said it had asked for access to Syrians returned to Turkey from Greece "to ensure people can benefit from effective international protection and to prevent risk of refoulement", referring to unlawful deportations of refugees at risk of persecution.

Ankara said it had maintained an open-door policy for Syrian migrants for five years and strictly abided by the "non-refoulement" principle.

"None of the Syrians that have demanded protection from our country are being sent back to their country by force," a foreign ministry official told Reuters.

But Amnesty said testimonies it had gathered in Turkey's southern border provinces suggested authorities had been rounding up and expelling groups of around 100 Syrian men, women and children almost daily since the middle of January.

"In their desperation to seal their borders, EU leaders have wilfully ignored the simplest of facts: Turkey is not a safe country for Syrian refugees and is getting less safe by the day," said John Dalhuisen, Amnesty International's director for Europe and Central Asia.

"The inhumanity and scale of the returns is truly shocking; Turkey should stop them immediately." 

Under the deal, Turkey is supposed to be taking in migrants returned from Greece on April 4, but uncertainty remains over how many will be sent back, how they will be processed, and where they will be housed.

The aim is to close the main route by which a million migrants and refugees crossed the Aegean Sea to Greece in the last year before heading north, mainly to Germany and Sweden.

Additional reporting by Reuters.