The National Audit Office (NAO) said in a report that most of the money was spent on staff costs, building new infrastructure and paying for external advice.
Although some ministries had to supplement their spending from existing budgets, the government overall only spent about 70% of the 6.3 billion pounds allocated to cover the cost of preparations, the report said.
In an indication of the upheaval that Brexit caused within government, the report said no fewer than 22,000 government officials were working on Brexit at the peak when Britain was on the verge of leaving the EU without a divorce deal last October.
“This report provides, for the first time, a clear picture of how much government has spent and what that money has been spent on,” said NAO head Gareth Davies.
Britain left the European Union at the end of January, its biggest geopolitical upheaval in decades in which it turned its back on 47 years of membership of the world’s largest trading bloc.
Officials had to increase training for customs officials, hire more staff to negotiate trade deals and improve infrastructure around ports.
More than half of the money was spent by three departments: Environment, Food and Rural Affairs and the Home Office, along with HM Revenue and Customs.
The NAO said their estimate only focused on the cost of government preparations and excluded future costs such as the 39 billion pound divorce bill agreed with the EU.
It also said the report does not come to a value-for-money conclusion, while there were limitations in the information provided by departments and the estimate is only the minimum level of spending by the government.
Lawmaker Meg Hillier, who chairs parliament’s public accounts committee, said the data was limited and that the finance ministry seemed unconcerned by the lack of transparency.
Overall, £1.9 billion was spent on paying government employees, £1.5 billion went on new infrastructure and £288 million was spent on external advice.
