This week the company announced more than 1,000 jobs were to go at its Belfast plant, which makes the wings for its new C-Series plane.
It is part of a cost-cutting drive that will see Bombardier shed 7,000 jobs across its global workforce.
Alastair Hamilton told the BBC's Inside Business programme he had confidence in management at the firm.
"I'd be pretty confident that if they are going to do a plan such as they've done over the last few days, that they will have that well thought through and they'll have built that to make sure that they are fit for the future," Mr Hamilton said.
Bombardier is one of Northern Ireland's largest private sector employers, providing jobs for 5,500 people and additional work for many other local suppliers.
It operates in four locations - east Belfast, Newtownabbey, Dunmurry and Newtownards.
The firm's significance to the economy is huge - it produces 10% of Northern Ireland's total manufacturing exports.
The company has been under severe financial pressure, as cost overruns on its new C-Series jet have drained cash out of the company.
"I think we're at a turning point for the C-Series," Mr Hamilton said.
"We've made our investment, we've made that investment at risk, we fully understand that, but this is about rebuilding this operation for a future of high-tech, high quality, composite-based manufacturing."
The head of Invest NI has said he is confident there will be no more job cuts at Bombardier in the near future.