Hundreds of civil service jobs dealing with Brexit negotiations have still not been filled just days before Britain formally begins the process of leaving the European Union, the National Audit Office has warned.

Many positions at the Department for Exiting the European Union (Dexeu) and the Department for International Trade (DfIT) are still vacant, causing concern over the government’s ability to handle the Brexit process.

“As of February 2017, the civil service has created over a thousand new roles in the new departments and elsewhere to prepare for exiting the EU and negotiating new trade agreements,” the National Audit Office said in a report.

“Two-thirds of the roles have been filled, mostly by transferring staff from elsewhere in government. There has not been a commensurate increase in the overall size of the civil service.”

The group said the civil service is already struggling to cope with major projects, and the government needs to show “greater urgency” in filling the gaps if it is to cope with the strain Brexit is expected to put on operations.

The government should even go as far as cancelling projects it is “not confident it has the capacity to deliver”.

NAO head Amyas Morse said: “Government has gaps in its capability and knows it must do more to develop the skills it needs.

“It is making plans to do so but the scale of the challenge ahead means greater urgency is needed.

“Without a short-term solution to its capability gaps, government must get better at planning and prioritising its activities and be prepared to stop work on those it is not confident it has the capability to deliver.”

The government confirmed this week it would trigger Article 50 of the Lisbon treaty on Wednesday 29 March, with Brexit Secretary David Davis saying: “We are on the threshold of the most important negotiation for this country for a generation.

“The Government is clear in its aims: a deal that works for every nation and region of the UK and indeed for all of Europe – a new, positive partnership between the UK and our friends and allies in the European Union.”