Prime Minister Theresa May has said Boeing's behaviour in its trade dispute with Bombardier is undermining its relationship with the UK.
She said Boeing was not adopting "the sort of behaviour we expect from a long-term partner".
Jobs in Belfast could be at risk after the US opted to impose a 220% import tariff on Bombardier's C-Series jet.
The move came after Boeing complained that Bombardier was receiving unfair state aid from the UK and Canada.
Canada's Bombardier is one of Northern Ireland's biggest employers and the threat to jobs there could jeopardise the Conservatives' pact with the Democratic Unionist Party.
Speaking at a Bank of England event in central London, Mrs May said there was also a wider issue.
"I think there is a real challenge for us globally today, because I think that there are aspects of protectionism creeping in around the world," she added, saying that she wanted the UK to be "a global champion of free trade".
In 2016, Boeing won a contract to supply 50 Apache helicopters to the British Army, which could now be scrapped.
In response to Mrs May's remarks, the opposition Labour party's international trade spokesman, Barry Gardiner, said she should refer the Boeing-Bombardier case to the World Trade Organization, instead of making an "empty threat" against Boeing.
The UK government and trade unions fear the imposition of tariffs could make the Canadian firm question whether to remain in Northern Ireland, where it employs 4,100 of its 28,000-strong workforce.
About 1,000 jobs are linked to the C-Series, the wings of which are made at a purpose-built £520m factory at Queen's Island in Belfast.
The programme is not just important to Bombardier jobs in Belfast, but also to 15 smaller aerospace firms in Northern Ireland - and dozens more across the UK - which make components for the wings.
The US Department of Commerce ruling, which could triple the cost of a C-Series aircraft sold into the US, could potentially jeopardise a major order placed last year from US airline Delta - a $5.6bn (£4.15bn) deal for up to 125 of the jets.
Bombardier said the decision was "divorced from the reality about the financing of multi-billion-dollar aircraft programmes".
The Canadian firm has said Boeing is seeking to use US trade laws "to stifle competition".