The Scottish Hospitality Group (SHG) said that staff have faced “intolerable levels of abuse” and some venues saw a drop in footfall of up to 40 per cent.
It is calling on the Scottish Government to scrap the scheme, which has been legally enforceable since October 18.
Proof of full vaccination is required to enter nightclubs and large events as part of the Scottish Government’s efforts to limit the spread of coronavirus and increase vaccine take-up.
The measures technically came into effect from October 1, but an 18-day grace period was announced following backlash from affected industries and significant problems with the new app.
SHG spokesman 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 Scottish Hospitality Group has been warning the government for weeks that their vaccine passports scheme is not ready but the government’s attitude has been to tell us to ‘get on with it’ whilst offering no safety net of support for businesses or our hard-working staff.
“The experience of this weekend shows that 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.”
The SHG comprises many restaurant and bar businesses, including the DRG Group, Buzzworks Holdings, Signature Pubs, Montpeliers and Manorview Group.
It said that over the weekend members reported more than 550 instances where venue staff had to refuse entry to a customer because they had no vaccine passport, an ineligible vaccine passport, or a potentially fraudulent vaccine passport.
There were also a “concerning number” of reports of abuse of hospitality staff over rejections and queues at venues, and continuing problems were reported with the vaccine passport app and its update.
The vaccine certification scheme applies to late-night premises with music, alcohol and dancing between midnight and 5am.
Mr Montgomery said the SHG is seeing some venues closing at midnight to “take themselves out of scope of the regulation for reasons around recruitment and staff welfare”.
He said: “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.”
A Scottish Government spokeswoman said: “Covid-19 certification is a proportionate way of encouraging people to get vaccinated, and also of helping large events and night-time hospitality to keep operating during what will potentially be a very difficult winter.
“This means many businesses will not have to close and can continue to trade whilst making necessary adjustments to ensure their premises are as safe as possible for staff and customers.
“Officials continue to engage regularly with the sector to discuss implementation of the scheme.”
The latest data from the Scottish Government reported that another 2,528 cases of coronavirus had been confirmed on Sunday.
There were 21 deaths recorded yesterday, though 20 of those were from Saturday with data issues causing a reporting delay.
Up to Sunday, 4,305,582 people had received the first dose of the Covid-19 vaccination and 3,892,224 had received their second dose.