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Ministers are facing demands for more honesty and transparency over any logjams at the UK border in the wake of Britain’s exit from the EU, amid concerns that waves of disruption will last for six months.

Several lorry drivers are understood to have been turned away at Dover for not having the right paperwork following the end of the Brexit transition period last week. It has caused concern among logistics and manufacturing companies that more severe problems could occur as trade flows increase later this month.

The main initial worries for businesses concern the availability of vets to carry out checks for new export health certificates. This could hit meat and food sales to the EU. Bigger challenges will come when freight starts flowing from manufacturers of complex products, which are unlikely to have begun using the new systems.

“We are going into a test period,” said Elizabeth de Jong of trade body Logistics UK. “If you were running your own business, you wouldn’t do it like this. You would have designed your new processes, you’d have trained people in them, you’d have tested the new systems, you’d have used it with dummy data, you’d have had a walkthrough. Those are all fundamentals of management. We’ve not been able to do any of it.

“There are also cliff edges ahead. In July, we’re going to start import checks as well: that will need more capacity and more people. We’ve also got grace periods in Northern Ireland.

“We need the absolute analysis of what’s going well, what isn’t, where the blockages are and what are the difficulties. We need that honesty and transparency. It’s a shared problem. We will get there and there are a lot of people who want this to work.”

As the Brexit transition period ended last Thursday, Boris Johnson hailed the new relationship with the EU as an opportunity to “transform our country”. Disruption was not expected over the weekend, with low levels of freight crossing the border. However, almost half of the lorries entering Belfast from Britain on the first ferry of New Year’s Day were inspected: one was stopped for three hours. Jean-Michel Thillier, customs director for Calais, has warned the new arrangements will face “trial by fire” when traffic increases.

In a move designed to curb queues, lorry drivers heading for mainland Europe must have a Kent Access Permit before entering the county. However, there are already reports that some holders of the permits still did not have all the necessary paperwork.

Johnson won the support of hardline Tory Eurosceptics for his Brexit trade deal, but there remains unease about Northern Ireland being treated differently from the rest of the UK and extra checks effectively creating a border in the Irish Sea. Northern Ireland secretary Brandon Lewis tweeted on Friday, however, that there was “no Irish Sea border”.

Labour leader Keir Starmer’s decision to back the Brexit deal – which led to three frontbench resignations – is still angering his MPs. Some said they were now completely unclear about Labour’s aims for improving Britain’s relationship with the EU. “The Labour MPs [who refused to back the Brexit deal] aren’t going away,” said one rebel. “They will absolutely want Labour to be looking again at a customs union with the EU.”

Former shadow cabinet member Clive Lewis warned that it would prove impossible for Labour to avoid the Brexit fallout. “The departure from Europe is going to open up a whole series of questions. A big part of the manifesto is going to have to talk about what we’re going to do with our relationship with Europe.”

Meanwhile, Nigel Farage’s Brexit Party – which is seeking permission to rebrand as Reform UK – is planning to use concerns about fishing in its local election campaign in May. But for now, with Farage having announced that the “war is over”, the party is planning to focus more on issues such as the government’s Covid strategy.

The Brexit party says it will field around 2,000 candidates in May’s local elections. However, chairman Richard Tice said he was already concerned there would be attempts to postpone the elections because of the pandemic.