Syrian refugees in Egypt are bearing the brunt of a sudden wave of xenophobia, in one of the more unexpected side effects of the removal of Mohamed Morsi from the Egyptian presidency.

Since Morsi's fall, Egypt's new government has turned away hundreds of Syrians from its borders, at times sending whole plane loads of refugees back to their airport of origin. Widely watched Egyptian television hosts have threatened Syrians with hate speech – all because Syrians have become unfairly associated with Morsi's hated Muslim Brotherhood.

Some Syrians report an increase in xenophobic street harassment, others greater job insecurity. One man claimed his children were not allowed to register at a state-run school because of their Syrian nationality.

In a recent development, many Syrians now fear deportation following a sudden round of arrests of Syrian refugees who had allowed their paperwork to slip during the lax Morsi administration.

"Of course Egypt has a right to reinforce their laws – but give us a heads-up," said Bouchra Zeinab, a prominent organiser in Cairo's Syrian community, who asked for her name to be changed to avoid reprisals from state security. "We're talking about people who are fleeing for their lives. They left Syria to escape being rounded up and arrested. Now that exact situation is happening to them here. They're being kicked while they're down."

At least 90,000 Syrians have fled to Egypt from Syria's civil war, according to official UN figures – while community organisers say the real figure could be above 300,000. Under Morsi, Syrians were allowed to enter Egypt with just their passports – and were greeted with open arms by the state and wider society.

"As soon as Syrians got to Egypt, in many respects they were considered as Egyptians – when it came to access to public schools and healthcare facilities," said Mohamed Dayri, the regional representative for the UN high commission for refugees (UNHCR).

The warm welcome led many Syrians to take a laissez-faire approach to registering as refugees with the UN, or to seeking official residency status from the Egyptian government. This left them caught off-guard by the new regime's sudden change in policy.

Since 8 July, five days after Morsi's fall, Egypt's military-backed regime has turned away those without prearranged visas – including Syrians already based in Egypt who were returning from brief trips abroad.

The turnaround in state policy came hand-in-hand with a wider volte face across Egyptian society. On 6 July, Tawfik Okasha, a reactionary television talk-show host, called on Egyptians to arrest any Syrians they found in the street.∑

Ammar, a Syrian video editor who asked for his surname to be withheld, said that his bosses had started to talk of firing the Syrian employees at his firm. "It could be coincidence. But I can't help but notice that we only started to hear about the possibility of firing Syrian employees after 30 June," said Ammar, referring to the date of the mass protests that led to Morsi's departure.

That week, Dana, a Syrian art student, was walking with Syrian friends through Tahrir Square in Cairo when they were stopped by vigilantes and handed over to the police. The police then interrogated her three times over the next five hours about her Syrian links. "When I first arrived at the police station, there were six Syrians," said Dana, who was eventually released. "But every time I walked out of one interrogation there were more and more Syrians detained. There were about 15."

Soon after, Alaa Soqair, a 45-year-old Syrian now living in Egypt, told reporters his four children had been turned away from a state school on the basis of their nationality. Egypt's military-backed regime has used nationalist rhetoric to justify its legitimacy and to alienate Morsi's Muslim Brotherhood, prompting a wave of xenophobia that has also targeted Palestinians and Americans. But Syrians have borne the brunt of the hatred because of the unfortunate way they became associated with Morsi in the dying days of his presidency.

On Saturday 15 June, Morsi shared a platform at a mass rally with hardline clerics who called for a holy war in Syria against the Syrian president, Bashar al-Assad. Some clerics also condemned the anti-Morsi protests on 30 June. In the minds of many Egyptians, the Syrian cause at that point became entwined with Morsi's – a perception reinforced by Morsi's subsequent decision to end diplomatic ties with Syria. "All in all, I think from that day Syrians were perceived to be supported by one political faction, headed by the presidency," Dayri said.

"The Syrians were used as a political pawn," said Zeinab, the Syrian community organiser. "What that speech essentially did was side thousands of Syrians inside Egypt with one faction against another. We were mortified."

Absurd rumours spread that Syrians were heavily involved in the pro-Morsi movement – leading to some Syrians being threatened with assault in the runup to 30 June. The situation worsened following Morsi's ousting, when a Syrian teenager was arrested on charges of taking part in Islamist demonstrations. Soon there were suggestions on some television channels that the main pro-Morsi sit-in in east Cairo was 60% staffed by Syrians.

Finally, last weekend the military set up roadblocks near the sit-in, allowing them to question dozens of Syrians on their way to and from work. Those who had not kept their papers up-to-date were arrested – sparking fears that many Syrians already living in Egypt will be deported.

Rights groups have called for Syrians to be given a month to legalise their status.

"This is an extremely vulnerable population struggling to make ends meet," said Priyanka Motaparthy, a Cairo-based researcher at Human Rights Watch. "They should be allowed a grace period to apply for residency."

Additional reporting by Mowaffaq Safadi