There is growing concern among key aerospace manufacturers about regulatory alignment and the ability to bring products to market after Brexit.
The firms have sought reassurance that the UK would continue to be a member of the European Aviation Safety Agency after any Brexit deal.
They also warned that alignment with chemicals regulations is "vital" for the sector.
The government said it would pursue agreements where necessary.
The government is facing a backlash from key manufacturers amid growing industrial concern that Boris Johnson's Brexit negotiators have dropped existing commitments to participate in specific EU regulatory institutions after any Brexit deal.
BBC News has obtained a letter from the aerospace industry body, the ADS, to the government asking for "reassurance" that "continued membership of the European Aviation Safety Agency (EASA) and alignment with EU chemicals regulations" which "are vital for our sector".
It said that "we received assurances from the previous [May] government that the UK would seek to continue membership of or retain participation and influence in EU agencies such as EASA".
The letter, dated this week, and sent to Cabinet Office minister Michael Gove and Brexit secretary Stephen Barclay, expresses "concern" that the PM has signalled a different approach.
Repeated attempts to get clarity on this issue have not reassured the aerospace and other industries on this topic.
It says that "regulatory divergence would pose a serious risk to our sectors" will result in "huge new costs and disruptions to many of our member companies", and an "inability to shape safety rule making" which "will make it much more difficult to bring UK technology to market".
In the existing political declaration on the future relationship between the UK and the EU, negotiated under Theresa May, there were specific references to ongoing close cooperation between a post-Brexit UK and three named regulatory agencies - the European Aviation Safety Agency, the European Chemical Agency as well as the European Medicines Agency.
The political declaration said "in this context the UK will consider aligning with [European] Union rules in relevant areas".
After the completion of negotiations, Mrs May confirmed to parliament that the political declaration meant for her negotiating a form of UK membership of these agencies which set technical specifications and safety standards across the whole European single market.
The concerns are shared in other industries, which have asked for similar reassurances, only to be told in recent weeks that the government is seeking a "best in class" free trade agreement, where the UK would set its own regulatory standards.
The government has acknowledged that it wants to take the "level playing field" arrangements out of the political declaration that promised alignment on environmental, social, labour and some tax measures.
These were also seen as crucial to ongoing industrial regulatory cooperation, and preventing the introduction of many types of checks on trade.
But the government fears such measures agreed by Theresa May will restrict the ability of a post-Brexit government to strike meaningful trade deals with other countries such as the US.
A source close to the negotiations acknowledged to the BBC that among changes being negotiated to the political declaration references to EU agencies could get scrapped.
Even as most of the negotiating attention remains on Northern Ireland, the change in approach from the Johnson government suggests a significantly different, more diverged end point for Brexit for England, Scotland and Wales, than envisaged under Theresa May.
A government spokesperson said: "The UK is getting ready for Brexit on 31 October. We want a deal, but we must be prepared for every eventuality and we have recently announced substantial extra funding to support businesses to get ready.
"The government is seeking a best in class FTA [free trade agreement] drawing on the precedent of existing EU FTA deals.
"We have been clear that we are committed to maintaining high standards after we leave the EU.
"Where necessary, the government will pursue additional agreements to cover areas outside traditional FTAs - for example, on aviation and civil nuclear cooperation."
A number of Labour MPs who say they want to support a deal have already expressed a desire for a deal with less scope for regulatory divergence.