FSB has criticised proposals to make those who meet MSPs, and are paid to do so, fill in returns and submit them to officials.
Individuals would also have to be pre-registered ahead of a meeting with a MSP.
Plans to establish a new register for lobbyists are being consulted on by the Scottish Government.
Ministers propose bringing in new legislation which would require lobbyists to sign up to the register before engaging with politicians.
The consultation comes ahead of the government’s proposed Lobbying Transparency Bill.
It could establish a register of consultant lobbyists, who carry out such work outside organisations or individuals, and in-house lobbyists who carry out lobbying work for their company as part of their role. Registration would be required before lobbying of MSPs or ministers can take place, with lobbyists required to submit periodic returns of their activities.
The legislation would cover those who have face-to-face dealings with politicians and would not apply to letters, phone calls or emails to MSPs and ministers. It has been suggested that trade unions and charities would be exempt from the legislation.
In its submission to Scottish Government consultation, the FSB claims the plans break the government’s own rules on better regulation and say MSPs should instead be publishing a list of their meetings at which they were lobbied.
The FSB fears member-led campaigning groups may be deterred from raising concerns with MSPs.
The business group said it condemned any suggestion that the motives of all charities and trade unions are automatically benign while those of the private sector are suspect.
Colin Borland, the FSB’s head of external affairs in Scotland, said: “We are told that Scottish democracy has never been healthier, so we’re not sure what problem the government is trying to solve.
“What we do know is that this will mean more red tape for small consultancies and an administrative nightmare for membership organisations.
“There is a particular problem for small business owners, who may belong to a local business group and regularly meet their local MSPs.
“However the law tries to define lobbying or a lobbyist – some will, some won’t be caught.
“We know that, where ambiguity exists, people err on the side of caution.
“We can’t have businesses withdrawing from public debate for fear of breaching the rules or because the bureaucratic burden is too great.”