Amman has begun a registration programme for hundreds of thousands of Syrian refugees that requires them to have their irises scanned or face being shut out of basic services within a year.

Jordan, which is reeling from a flood of refugees, began a major operation to count the number of Syrians living in the country yesterday. It comes as the country, concerned about its own stability, has increased deportations of Syrians it deems to be a security threat.

The programme aims to formalise Syrians’ residency by providing a new services card that allows them to open bank accounts and register their children for school.

However, to get the card, Syrians must present themselves at a police station for an iris scan and identity check.

Walking into a police station can be a terrifying experience for many refugees. False documents are common among the refugee population, and fears over presenting those documents, potentially leading to deportation, will dissuade some from coming forward.

While the number of arrivals is beginning to stabilise as the authorities exercise greater control over the country’s borders, there is little clarity over how many people are there. The UNHCR has registered 613,000, yet Jordan claims there are 1.2 million.

The UNHCR hopes that despite its risks, the new programme will make refugees’ lives easier. “It’s in everyone’s interests to have a better understanding of who is here, what their needs are and to ensure aid and protection are delivered as efficiently as possible,” said Andrew Harper, the head of UNHCR’s Jordan operation. However, the deportation of Syrian refugees concerns human rights organisations.

There is also the matter of a 30 dinar (£27) fee for a blood test, a standard requirement for residency in Jordan but a deterrent to refugees without means.

Jordan says that as well as offering clarity about the number of people within the country, the exercise could bring in badly needed aid funding.