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Sir Simon said during a House of Commons Committee hearing that "civil servants don't feel they have clear political direction at the moment," and some are thinking of quitting their posts.
In a report by the Financial Times, several civil servants backed up Sir Simon's claim by saying they are preparing to quit. One told the paper: "I've done my best."
Ever since Theresa May took over from David Cameron as prime minister in July, she has given little detail about what post-Brexit Britain might look like, saying only that: "Brexit means Brexit." She has put together a cabinet of both Brexiteers and Remain supporters and said she intends to trigger Article 50 by March 2017, which would start the two-year exit negotiation period.
However, what happens once negotiations begin is far from clear. A leaked note on Tuesday from consultancy Deloitte claimed the government has no clear Brexit plan and Prime Minister Theresa May's cabinet cannot stop disagreeing with each other.
It added that "individual departments have been busily developing their projects to implement Brexit, resulting in well over 500 projects, which are beyond the capacity and capability of government to execute quickly" and said the government could "need to hire 30,000 extra civil servants."
The government insisted the memo was an unsolicited piece of business fishing by Deloitte, but did little to dispute its contents.
Even the most basic part of the Brexit process - triggering Article 50 - has been fraught with problems. At the beginning of November, London's High Court rules that May must get parliamentary approval before invoking Article 50. It creates a clear and legal way for parliament to block May from triggering Article 50, thereby delaying the start of the two-year negotiation process for a Brexit.
The government confirmed that it will be appealing the decision, which means the case will be transferred to the Supreme Court in December this year. It will be the first time the Supreme Court sits in full since its establishment in 2009.