It was appropriate to deprioritise emergency preparations before the pandemic in order to plan for a no-deal Brexit, the deputy prime minister has said.

Speaking at the Covid-19 inquiry in London, Oliver Dowden has defended the decision to pause some emergency planning in order to work on Operation Yellowhammer, the cross-government preparation for Britain’s no-deal exit from the EU.

Dowden told the inquiry on Wednesday this was a direction from Boris Johnson, who was prime minister at the time.

“It is worth remembering the kinds of frankly apocryphal warnings that were being delivered about the consequences of no-deal Brexit, for example, in relation to medical supplies,” he said. “It was appropriate that we shifted the resilience function to deal with this.”

The inquiry saw an internal document from the Cabinet Office that said it was “prioritising no-deal preparation from now on”.

Its department for emergency planning, the Civil Contingencies Secretariat (CCS), would “continue a small number of essential activities” but had “paused all other activity to enable sufficient focus on preparations for leaving the EU without a deal”, it said.

Katharine Hammond, former director of the CCS, had previously told the inquiry that preparation for a no-deal Brexit was “a really major consumer of resources in [her] time” and described it as creating “unprecedented resource pressure” in another document shown to the inquiry.

But, asked whether preparing for a no-deal Brexit significantly impacted the planning for an influenza pandemic, Dowden said that he “takes a different view given my experiences and minister at the time”.

“If we hadn't done that reprioritisation, we would have been in a much worse position to deal with Covid when it hit had no deal actually occurred,” he said.

“This was part of a normal, routine prioritisation – albeit, I should say, the more extreme end of reprioritisation given the amount of resources we had to dedicate to no deal since it wasn’t one-sector-specific.”

Dowden was speaking during the first module of the Covid-19 inquiry, which is seeking to explore the UK’s preparedness for the pandemic. Chancellor and former health secretary Jeremy Hunt will give evidence this afternoon.

The inquiry continues.