The PM said he would prefer to get a deal with the EU, but he said he recognised this “may not happen”.
Earlier Jeremy Corbyn had urged the UK’s top civil servant to intervene to prevent a no-deal Brexit happening during a general election campaign.
It comes amid speculation MPs could back a no-confidence motion in the PM.
In his letter to civil servants, Mr Johnson said the UK must be prepared to leave the EU by the latest Brexit deadline of 31 October “whatever the circumstances”.
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“That is why preparing urgently and rapidly for the possibility of an exit without a deal will be my top priority, and it will be the top priority for the civil service too.”
It is understood that government special advisers also received an email last night from the PM’s senior adviser Eddie Lister instructing them not to take annual leave until after 31 October.