Jordan is home to over half a million Iraqi refugees or asylum-seekers and they are placing a considerable burden on public services, especially health and education.
The government has tried to reduce the influx by barring those aged 18-45 from entry and making it harder for those in the country to obtain permanent residency.
Last month Iraq gave Jordan US$8 million to help it cope with the burden of Iraqi migrants, but Interior Ministry officials say the concern is not purely economic.
"The concern now is that terrorists could enter and do damage in the kingdom," said an official from the ministry who did not wish to be named.
In 2005 a suicide attack on three hotels in Amman killed at least 60 people and injured 100 others. The attack was carried out by two suicide bombers, both Iraqis.
The new visa regime is meant to regulate the flow of migrants and allow security personnel to conduct thorough checks prior to arrival, according to Interior Ministry officials.
Over the past four years, no fewer than 700,000 Iraqis are believed to have entered Jordan to seek refuge from the violence in their home country. Many Iraqis have moved on to settle in third countries, but up to 500,000 have settled in Jordan.
Iraqi and Jordanian officials say the visa regulations have been put in place for humanitarian reasons, in a bid to ensure that all passengers who show up at the border are allowed in: Iraqi officials had complained that Iraqis trying to enter Jordan had been treated badly and forced to wait for hours, and sometimes days, before being told whether they could enter or not.
"The visa system is good for Iraqis because they will not have to stay in the cold or heat at the mercy of border officials," said Iraqi ambassador to Jordan Saad Hayani.