The Federation of Small Businesses (FSB) survey found 50 per cent were against an extension while 26 per cent backed it.
About a quarter of of the 513 respondents (24 per cent) did not offer an opinion.
However, more than three quarters (78 per cent) of hospitality and leisure sector respondents are opposed to an extension with only one in ten (11 per cent) supportive.
Deputy First Minister John Swinney said on Tuesday the Scottish Government was considering extending the vaccine certification scheme – already in place in nightclubs and at other large events – to more of the hospitality and leisure sector.
He stressed a decision had not yet been made, but said Covid-19 was at a “concerningly high level” and Scotland was in a “precarious and unpredictable” situation in the fight against the virus.
The FSB opened the online poll on its website on Thursday, closing at 11:30am on Friday.
It found the among the 92 hospitality and leisure businesses which responded, 90 per cent believe extending the scheme would hit takings and 62 per cent believe it would increase overheads.
Some three-quarters believe it could cause increased conflict with customers, while 10 per cent said it would lead to a positive response from staff and customers.
Andrew McRae, FSB’s Scotland policy chair, said: “Every minute spent administering the vaccine passport scheme is time that can’t be spent elsewhere in the business.
“So this could be a real headache for the small cafes, restaurants and pubs already facing a shortfall in workers.
“The Scottish Government justified their current vaccine passport scheme by arguing it would be focused on a small number of the largest, highest risk operators.
“We would ask ministers to carefully consider whether extending the scheme to smaller lower-risk operators is the right move when many of these firms are already under pressure.”
Earlier this week, business leaders and opposition politicians at Holyrood reacted angrily to the prospect of an extension, with the Scottish Chambers of Commerce insisting it would be a “massive step backwards”.
Scottish Conservative economy spokeswoman Liz Smith said: “The FSB’s polling demonstrates just how damaging any extension of the vaccine passport scheme would be for small Scottish businesses.”
She added: “The SNP’s shambolic vaccine passport scheme is already causing significant financial damage to the businesses it currently applies to – any move to widen its scope would be disastrous for our economic recovery.”