On his “first working day” in office, Donald Trump signed a presidential memorandum to freeze hiring of non-military federal workers in a move applauded by small government conservatives and lambasted by public sector workers.

The order mandates that “no vacant positions existing at noon on January 22, 2017 may be filled and no new positions may be created” until the president implements a longer-term plan to cut the federal government workforce by attrition.

Although the measure is only temporary, it may have potentially unintended consequences for one of Trump’s most aggressive policy reform platforms: tough immigration enforcement and ramped up deportations.

The order includes exemptions for any government hires tasked with “national security or public safety responsibilities”, meaning Trump can still go ahead with pledges to add thousands of new positions with the Border Patrol and Immigration and Customs Enforcement. But it is decidedly unclear how the freeze will affect the ultimate arbiter in hundreds of thousands of removal cases: the federal immigration courts.

These 58 courts are at a breaking point. With a backlog of over 530,000 cases, the highest number on record, the average case now takes close to two years to be processed and in some jurisdictions cases can languish in the pile for six years or more.

For many of the thousands awaiting an outcome on asylum claims, advocates warn, the uncertainty and prolonged limbo leads to serious psychological harm. Parties on both sides of the debate on immigration reform accept the situation is untenable.

As Trump looks set to preside over a hardline immigration regime, with pledges to speed up removals and ramp up enforcement within the United States, the backlog in these courts is likely to increase. This presents a setback for his enforcement pledges that would be significantly magnified if the federal employment freeze is applied to the Executive Office for Immigration Review [EOIR] – the justice department division responsible for immigration courts. Put simply, the order has the potential to slow down some of the deportations Trump has pledged to carry through.

The courts have remained chronically underfunded and understaffed as the backlog has continued to grow. Although EOIR went on a recent hiring spree, bringing the total number of judges in the system to a record high of 296, estimates suggest the department needs to hire another 150 judges to bring the backlog under control by 2023.

Even immigration hawks concede the federal hiring freeze could be a stumbling block for Trump. “If the goal is to reduce the backlog as quickly as possible, then yeah, a hiring freeze probably would make that harder,” said Mark Krikorian, executive director at the conservative thinktank the Center for Immigration Studies.

Others point to a bleaker potential outcome.

“If we’re not going to be hiring more immigration judges, then what we’re going to see is that backlog is going to expand and make for a very frustrating experience for folks regardless of what their political perspectives are. Those courts might very well come to a halt,” said César Cuauhtémoc García Hernández, an assistant professor at the University of Denver Sturm College of Law.

The Trump administration could seek to move EOIR into the public safety exemption category of the presidential memo, but the Guardian has learned that the National Association of Immigration Judges, the professional organisation representing immigration jurists across the US, has received no guidance on the matter.

García Hernández argued that such a move would not be “an intuitive reading” of the exemptions.

“It would seem to strain logic, but simply because it’s a strain of logic, as we’ve learned, doesn’t mean that it’s off limits. It may be, if I can paraphrase Kellyanne Conway, simply an alternative reading of logic,” García Hernández said.