All four nations of the UK have seen a huge decrease in applications since Brexit came into force this year, whilst the number of non-EU students accepted to British universities has seen a significant increase.
Alyn Smith MP told the SNP conference there was growing "enthusiasm for independence in Europe".
The deal sees Greens form part of the government for the first time anywhere in the UK.
In response to Labour and Tory backlash a spokesman for the Scottish Greens said: “It’s no surprise that parties only interested in scoring political points would be alarmed about any suggestion of co-operation in the interests of people and planet."