The Scottish Hospitality Group (SHG), which represents a number of pubs, bars, nightclubs and restaurants, also issued a fresh call for the scheme to be scrapped.
The legal requirement of vaccine passports for entry into night-time venues came into force on Monday 18 October.
Information from the SHG found more than 550 incidents where staff had to reject entry due to guests not having the vaccine passport, it being ineligible or potentially fraudulent. It also claimed there were a "concerning number of reports of abuse of hospitality staff over rejections and queues at venues".
No safety net
Furthermore, businesses reported a drop in footfall of up to 40%, particularly in venues that normally close at 2am and did not previously need door staff.
SHG spokesperson Stephen Montgomery said: "The first weekend of the vaccine passports scheme has been one of unmitigated disaster – and that responsibility lies entirely at the door of the Scottish Government.
"The SHG has been warning the Government for weeks their vaccine passports scheme is not ready - but the Government's attitude has been to tell us to 'get on with it' while offering no safety net of support for businesses or our hard working staff.
“The experience of this weekend shows the result has been intolerable levels of abuse of our staff, and the creation of an atmosphere that will totally undermine anyone's enjoyment of our night-time venues.”
Scheme scrapping call
The research from the trade body also found venues being forced to close at midnight to take themselves out of scope of the regulation for reasons around recruitment and staff welfare.
Montgomery added: “How can we rebuild customer confidence when we are the ones being faced with the customer anger and confusion, while being made to enforce this policy in law, which has been made simply to increase vaccination levels in the younger demographic?
"The reality is that it's not vaccine passports that will end this health crisis – [the] Government themselves have acknowledged that the solution is an acceleration of booster vaccinations.
“The Scottish hospitality industry as a whole, has paid enough for Government failures in this pandemic, and it's time the Scottish Government scrapped this scheme altogether."