Doncaster also warned of the “considerable additional cost” involved for clubs as he addressed the Scottish Government's Covid-19 committee ahead of the planned implementation of vaccine certificates for large scale outdoor events attended by more than 10,000 people on October 1.
He stressed that any technological solution is "untried and untested" and that affected clubs - including Rangers, Celtic, Aberdeen, Hearts and Hibs, as well as the Scottish national side - should be allowed to manage their own approach to vaccine passports given the lack of time to plan.
Doncaster told MSPs: "In terms of stewarding there is a real shortage of security staff and stewards within the market and creating an outer cordon which is the only realistic way we believe of implementing such a spot checking scheme clearly will require a great many more stewards.
"I had discussions with a number of the clubs who would be involved and they believe that the costs purely in terms of stewarding and infrastructure will be upwards of £5,000 per game and that is before any technology costs.
"The only certainty is that there will be considerable additional cost and clearly we are in dialogue with Scottish Government officials as to what extent there may be support for those additional costs.”
Doncaster had previously said that the SPFL was "concerned" about the practicalities of delivering the scheme, warning it risked fan "disorder", and that spot-checking is the only way it can be done.
It comes after plans to introduce vaccine certificates in England were scrapped.