The head of the Home Office section that detains and processes asylum seekers for deportation to Rwanda has halted recruitment and is drawing up plans for staff cuts after demands from Jeremy Hunt, leaked documents show.

Stuart Skeates, the director general for strategic operations at Illegal Migration Operations Command (IMOC), wrote to colleagues on Tuesday to say his department had been told to cut the numbers of staff to “pre-pandemic levels”, in line with the chancellor’s plans.

In an email, Skeates said he “had not anticipated” that the department, central to Rishi Sunak’s immigration policy, would be asked to make the cuts demanded of others in Whitehall.

IMOC job vacancies have already been taken down from its website. The Home Office is also “urgently reviewing” job offers to people who have not yet started in their roles, the leaked documents show.

Home Office insiders are shocked at the decision, which comes just weeks before the first flight is expected to take off for Kigali.

The IMOC, formed to implement the Illegal Migration Act by processing and screening asylum seekers, is crucial to implementing the government’s Rwanda programme, a cornerstone of Sunak’s “stop the boats” strategy.

Skeates, who has worked on small boats and migration since January 2022, wrote in the email that he was “incredibly proud” of preparations for “the first flights to Rwanda commencement of the illegal Migration Act Duty to Remove provisions”.

“The chancellor has asked all departments to look at where it might be possible to reduce the overall headcount of civil servants. This will mean that we will have a designated headcount budget, the number of people we can have in post, and that we need to reduce our headcount to reach that cap.”

He wrote that “decisions will impact on people at all grades in IMOC and we will need to support one another”.

As well as cutting overall headcount, Skeates announced a recruitment freeze.

“I am taking the difficult decision today to temporarily pause new recruitment campaigns in the IMOC until we have finalised our plans for delivering against our headcount cap,” he wrote.

“I will also have to go a little further, specifically not progressing ongoing recruitment campaigns to ‘offer’ stages and urgently reviewing the job offers that have already been made but where the individual has not started in the new role.”

In October Hunt announced a “civil service numbers cap”, with expansion frozen and a plan put in place to return it to pre-pandemic size. At the time, he said departments would be asked to produce plans “on driving down headcount over the long term”.

The 2023 Illegal Migration Act is a key part of the UK government’s plan to stop asylum seekers crossing the Channel in small boats. It created laws that mean the home secretary must detain and remove anyone who arrives by that route.

A Home Office spokesperson said: “As with all government departments, we remain committed to accessing the best talent and skills into the civil service while adhering to headcount caps, maximising efficiency and delivering for the public whilst retaining maximum value for the taxpayer.”