Reports suggest new rules may permit driving the farm vehicles for as little as half an hour in certain circumstances. However, the Health and Safety Executive (HSE) has denied this.
The warning came as ministers admit they are prepared to fight new European regulations if they limit the time farmers and crofters can spend on their tractors to less than one hour a day.
Health and safety measures for whole-body vibration (WBV) limits were introduced in 2005 to protect workers from risks to health from vibrations. However, these are only to become mandatory next year for farm machinery built before 2007 when an exemption expires in July.
Patrick Krause, chief executive of the Scottish Crofting Federation, said: "The vast majority of crofters have tractors that were built before 2007 and (their machines) won't comply. So we will have to try to get an exemption. Crofters also have very much smaller tractors than those used on large farms.
"Will an old grey Ferguson tractor have the same vibrations as a 2000hp machine? So there may be an argument for seeking an exemption on the grounds of size as well. We need clarity on this."
Scottish Liberal Democrat MEP George Lyon said there was an "overwhelming case" for exemptions from these rules for Scottish farmers, but the 12,000 crofters, many who work alone, feel particularly vulnerable.
Donnie MacDonald, chairman of the Crofters Of The Isles, said: "The WBV restrictions would mean a crofter ploughing his field, which produces the highest level of vibrations apparently, might be allowed only half an hour each day on his tractor. No longer will he be able to take home his peats on the same day. It could take him a week or more."
However, Holyrood ministers are prepared to oppose any excessive restrictions. A Scottish Government spokesman said it would resist any "disproportionate or unreasonable" proposals.
He added: "The current regulation allows for exposure above the maximum so long as this is reasonably practical. It has allowed farmers and crofters to find a balance to lessen the risk as much as possible and let the industry flourish without impossible red tape. We will be looking to achieve a similar approach when the current exemption expires in 2014."
He said farmers and crofters realised the importance of reducing the risk of back pain and the industry had introduced training to limit this exposure.
He added: "With much of the farming calendar depending on daily weather patterns, it is impossible to limit how long farmers can be exposed to vibration to those currently recommended. The Government is aware of this issue and will be discussing the possible implications with the HSE."
An HSE spokesman said: "Our research shows few on-farm activities exceed the exposure limits during an average working day. If farmers are following the advice outlined in the long-standing HSE guidance the regulations should not require significant changes to established working practices."
He said that even for those using older machines there were some simple steps to reduce vibration levels.