In December, May chose to postpone a parliamentary vote meant to ratify the agreement at the last minute after it became clear that it would be overwhelmingly defeated in the House of Commons.
The DfT believes the use of Manston will be crucial in the event of disruption, but fears have grown locally that it would take several hours for lorries held at the site to leave, causing congestion elsewhere in the area.
"We are pretty much where we were before Christmas, with the proviso that there's less time left.
The closer we get to 29 March without a deal, the more assets will be transferred and headcount hired locally or relocated".
May's government has repeatedly warned that a no deal will lead to severe economic disruption, and on Monday the transport ministry was planning to test the road network to Dover, Europe's busiest ferry port.
A spokeswoman for the DfT said: "We do not want or expect a no deal scenario and continue to work hard to deliver a deal with the EU".
Liberal Democrat MP Layla Moran, of the anti-Brexit Best For Britain campaign, said it was a "taxpayer-funded farce" while shadow transport secretary Andy McDonald said it was "beyond parody".
May slammed MPs asking for a second referendum.
Asked if he could guarantee that no one would die as a result of a no-deal Brexit, Mr Hancock told Sky News' Sophy Ridge On Sunday: "I'm confident that we will have the unhindered supply of medicines so long as the plans that we have in place are properly enacted".
But it drew criticism for only involving 89 trucks and haulage companies dismissed it as "too little too late".
Theresa May has warned the United Kingdom will be in "uncharted territory" if MPs do not back her Brexit plan. "At this late stage it looks like window dressing".
This, in theory, could help strengthen the Conservative's grip on government with newly elected MPs potentially helping to strengthen Mrs May's deal in the event of a further vote.
With Tory rebels and her DUP allies expected to oppose it, the Prime Minister hopes to win round some Labour MPs alarmed at the prospect of a no-deal Brexit. The EU has signalled it may try to allay the fears of May's critics but will not renegotiate the deal.
MPs will vote on 15 January on whether to accept the legally-binding terms of withdrawal negotiated by Mrs May, as well as a framework of future relations with the EU.
May's Brexit deal is unpopular with British lawmakers across the spectrum, and the main sticking point is the insurance policy known as the "backstop" - a measure that would keep the United Kingdom tied to European Union customs rules in order to guarantee there is no hard border between the Republic of Ireland, an European Union member, and the U.K.'s Northern Ireland, which won't belong to the bloc after Brexit.
The UK government staged a "fake traffic jam" in Kent on Monday morning, with lorries queuing all the way to Dover, to establish the implications of Britain leaving the European Union without a deal, leading to ridicule on social media.