Mr Pirotte was speaking ahead of the launch of Medr's first strategic plan, eight months after it was set up in August 2024.
With a budget of £960m, it has taken over responsibility for funding and regulating universities, further education and training as well as school sixth forms.
The Welsh government has tasked Medr with looking at what subjects are offered by Wales' eight universities after Cardiff University said it planned to cut whole departments including nursing, modern languages and music.
Mr Pirotte said it was possible that universities could get more money to teach some subjects that could be in danger of disappearing altogether in Wales.
He said Medr did not have the powers to tell a university "that you can't delete subject X or you have to do subject Y" but it could advise the government where a subject may be "vulnerable".
He said it could raise questions about "what we want as a nation".
"Are we comfortable that certain provision may not be available in Wales and if Welsh learners or other learners wanted to access them that they'd need to go to an area outside of Wales?" he said.
"Or do we think that those things are of strategic or cultural importance to us in Wales in which case, what could we do in terms of incentivising that provision and making sure that it's still there for the future?"
Further and Higher Education Minister Vikki Howells has also asked Medr to investigate the impact of competition law on universities – "we're interested in collaboration and working together, but obviously that needs to be done within the spirit of competition law", said Mr Pirotte.