The British official who was in charge of Brexit border plans has warned that contingency planning for a no-deal departure “doesn’t mean … everything will be fine”.

Karen Wheeler, a former director general of Her Majesty’s Revenue and Customs Brexit border delivery group, said no-deal emergency plans would have to be stepped up again immediately if they were to be effective.

She said the civil service had done all it could to prepare for no deal, but that might not be enough to prevent chaos at Dover or on the Irish border.

Referring to the intense and detailed work carried out in Whitehall on contingency planning for the first scheduled Brexit day on 29 March, she said: “I think we felt we had done everything we could to mitigate as far as we could, but there were some areas of no deal where really the consequences did feel particularly difficult.

“Of course, goods and trade at the channel and Northern Ireland was one of the other areas where you can’t mitigate and all you can do is cope with the consequences.”

Asked what being ready for no deal meant, she responded: “What it doesn’t mean is everything will be fine.”

Speaking at an Institute for Government event in London on Wednesday, she said that when “the government says it is ready”, it is talking about having the processes and systems in place for a no-deal Brexit, but ministers and officials cannot predict how businesses, shoppers and people will react.

“What we can’t do is ensure that every other aspect will work, every other aspect of industry will work and be prepared,” Wheeler said.

About 6,000 civil servants were drafted in to work on no-deal preparations after Christmas, but were stood down in April, much to the annoyance of Brexiters, one of whom, the Conservative MP Steve Baker, said this was “sheer spite”.

Asked about the mood in Whitehall in March, Wheeler said: “It felt like we were preparing for a crisis, where we didn’t fully, couldn’t fully understand how it would play out, but we all felt every part of government felt it had its plans in place, it knew what it needed to do, it knew what the critical areas were with the biggest plans in place,” she said.

However, Wheeler said it was “extremely difficult” for British civil servants to plan for the effects of a no-deal Brexit in Northern Ireland because they were not able to speak to Irish civil servants about their plans.

One of the biggest issues yet to be resolved is how to conduct mandatory health checks on animals and agrifood being traded across the border. EU officials have said these need to be in place from day one.

She was also cautious about the report by the alternative arrangements commission, chaired by the Tory MPs Nicky Morgan and Greg Hands, that technology enabling an open border in Ireland would be ready in three years.

“Technology alone is not going to solve that border problem,” Wheeler said. “[It] has to be done in a way that works on both sides of the border, which is extremely difficult to achieve when we are not able to discuss these things with Irish colleagues.”

She said the European commission had made it clear in private conversation and felt “very strongly” that it would be treating the UK as a third country with “everything that entailed”, including “customs, quality of goods, controls and checks of agrifoods” from day one.