BMW UK chief Ian Robertson said uncertainty could damage the competitiveness of the UK's automotive industry.
The German carmaker employs around 8,000 people in the UK, with its plant in Oxford producing the popular Mini range.
It follows a warning by Airbus, employs 14,000 people across the country, that it could pull out of the UK with the loss of thousands of jobs if Britain crashes out of the EU without a transition deal.
The firm sent shockwaves throughout British industry and the Government when it said it would "reconsider its investments in the UK, and its long-term footprint in the country" if Britain was forced to leave the single market and customs union in March 2019 without any transition agreement in place.
Katherine Bennett, Airbus's senior vice president in the UK, told the Press Association: "We don't deal in idle threats. We seriously believe a no-deal Brexit would be catastrophic."
But security minister Ben Wallace hit back, saying the firm had relied on countries such as the UK to cover the costs of the A400M military transport plane.
Ministers have been told that the impact of exiting the EU without any sort of trade deal would be "devastating" for the aerospace industry.
Airbus has more than 4,000 suppliers, and its warning applies to other sectors such as automotive.
Mr Robertson said uncertainty was causing problems for the car industry.
He told the BBC: "If we don't get clarity in the next couple of months, we have to start making those contingency plans - which means investing money in systems that we might not need, in warehouses that might not be usable in the future, in effectively making the UK automotive industry less competitive than it is in a very competitive world right now."
The Government insisted the negotiations with Brussels were making "good progress" and it was confident that a "no-deal scenario" would not arise.
But unions and opposition parties attacked the Government for the impact already being felt across industry from the lack of a deal.
Airbus said it had been trying to raise its concerns about where the negotiations were heading for the past year without success.
It published a risk assessment warning that production is likely to be "severely disrupted" if there is no deal, leading to "unrecoverable delays", potentially costing Airbus billions of pounds.
If an agreement is reached, there would still be a "significant amount of risk", the company said, calling on the Government to extend the planned transition period due to run until December 2020.
A Government spokeswoman said that while officials were working closely with companies to understand their concerns, they did not expect a no-deal scenario to arise.
"We have made significant progress towards agreeing a deep and special partnership with the EU to ensure trade remains as free and frictionless as possible, including in the aerospace sector, and we're confident of getting a good deal that is mutually beneficial."
Downing Street denied that ministers had ignored concerns raised by Airbus about the Brexit negotiations.
"Airbus were in Downing Street with the PM in April as part of an aerospace round table," a spokeswoman said.
"(Business Secretary) Greg Clark spoke to them earlier this week and officials will speak to them today so we are listening to their concerns."
Additional reporting by Press Association.