Deirdre Michie, chief executive of Offshore Energies UK (OEUK), formerly Oil and Gas UK, said the current situation causes "confusion".
It came as OEUK warned the UK will have to import the vast majority of its oil and gas from overseas unless billions of pounds are invested in the North Sea.
Ms Michie said the controversial Cambo oil field off Shetland "and all other new projects like that" should go ahead.
The Greens, who have a power sharing agreement with the SNP, are outspoken in their opposition to new oil and gas drilling.
Patrick Harvie, the party’s co-leader and a Scottish Government minister, was previously criticised after he said it was "only the hard right who continue to deny the reality that" continued oil and gas extraction is "simply not compatible" with tackling climate change.
Asked if she worried about the influence of the Greens in government, Ms Michie said: "I think it's important that they're very clear when they are speaking for the Scottish Government and when they're speaking for themselves.
"And I think that does cause confusion.
"So when they're speaking for the Scottish Government, we need to be clear what they're saying, why they're saying it.
"But again, as Scottish Government ministers I'd like to think that they do understand the positive contribution that the sector is making, and the positive contribution that the sector is trying to drive."
Elsewhere, Ms Michie said she recognised the concern of school climate strikers.
However, she added: "I would say to these folk, I think you could progress your agenda if you were more supportive of what we're trying to do, rather than just wanting to shut us down.”
A Greens spokesman said the party’s agreement with the SNP “acknowledges different views to the long term future of oil and gas, but the First Minister herself is clear that a just transition needs to begin, something supported by a majority of the public”.
He added: “The Scottish Greens leaders are very clear when they speak in their capacity as government ministers.”