The City Region Deal – which aims to inject up to £2 billion of public money into the regional economy – is said to have been thrown into chaos by the vote.
Green economy spokesman Cllr Gavin Corbett said: “The City Region Deal has been in preparation for almost two years now and is due for final submission to UK and Scottish Governments in the late summer.
“The City Deal offers a massive opportunity to forge a new kind of low carbon, jobs-rich, high-skilled economy through major investment in transport and public places and building on the region’s natural strengths such as its universities and food production.
“It is a once-in-a-generation chance to transform the regional economy, but the UK exit vote comes at exactly the wrong time, for three main reasons.
“First of all, it leaves a period of deep political instability at a time when the UK Government needs to be making real long-term decisions.
“Secondly, it jettisons the role which EU programmes have played for a long time in investing in infrastructure, pioneering new standards of low carbon development, encouraging labour mobility and easing international exchange of ideas in universities.
“And thirdly, it sends a signal to would-be investors that the UK is turning in on itself, and declining to learn from the best of our international competitors.
“Both UK and Scottish Governments need to make very firm statements soon that long term investment will not be compromised by the shock referendum result.”
The City Council will debate the City Region Deal at its next full meeting on Thursday, 30 June.