The UK’s capacity to secure the best free trade deals after Brexit has been thrown into doubt by figures showing only around 30 civil servants attended a session on how to negotiate a trade agreement.

The revelation came in a report by MPs on the foreign affairs select committee, in which the body responsible for training free trade negotiators said it had intended to train 240 staff up to expert standard by Brexit day on March next year, but so far only 90 were at that level.

The head of the Diplomatic Academy, Jon Benjamin, told the committee the targets were challenging, adding: “We will be dealing with counterpart officials in other countries who may have been doing this for many years,perhaps exclusively so.”

Some have claimed that the withdrawal agreement negotiated by Theresa May severely hampers the UK’s ability to negotiate free trade deals independent of the EU. Donald Trump implied on Monday that the EU had negotiated a Brexit deal with the UK that left it unable to strike free trade deals with the US, a point strongly contested by Downing Street.

But the slow progress in training up trade negotiators, a job that was left to the European Union for the past 40 years, has raised questions about whether the UK was equipped to negotiate free trade deals around the world, even if it became legally entitled to do so.

Benjamin said he had hoped to reach the 240 target, “even if the date has to slip a little”. Asked to explain how many staff had been trained specifically in the skills of negotiation, as opposed to the technicalities of a trade deal, the committee was told “over 30” had attended a session specifically on negotiation skills.

The Foreign Office in its submission to the inquiry conceded the importance of negotiating expertise, adding: “The scale of the UK’s challenge in building trade capability from a very modest base is unparalleled amongst developed countries.”

A special trade negotiations and policy faculty with a budget of £1.9m has been established inside the academy. Benjamin said “a core of 90 people have been trained so far to expert level” adding “that effectively means, we hope, they are ready to negotiate the nuts and bolts of UK independent trade agreements in the future”.

It was not clear why there had been such slow progress in building a body of expert trade negotiators, but the report highlighted a problem of low pay. It said that across the Foreign Office civil servants were being asked to produce Premier League-level service based on Championship-level salaries.

The committee described the problem of relative low pay inside the Foreign Office as alarming, unsustainable and deep rooted.

The department, drawing on data from the Cabinet Office, revealed it paid the lowest median of any central government department for policy officers and middle management officers, with 70% of those leaving citing poor pay as the main reason.

The committee urged the government to look at options for improving the pay offer at the Foreign Office, both for centrally contracted staff and for local hires abroad.