The Association of Personal Injury Lawyers (Apil) believes the shortfall will come due to Government plans to move more than 2000 cases a year from the Court of Session to the sheriff court.
The average Court of Session fee for a personal injury case is more than £500 higher than the average sheriff court fee, according to figures obtained by the Apil under the Freedom of Information Act, and the organisation said the difference would result in a shortfall of about £1m in annual income.
The Scottish Government plans to set "realistic fees based on services" aimed at eventually covering the costs of running courts as part the shake-up, which forms part of the Courts Reform (Scotland) Bill.
But Apil fears this will result in fees to claimants and pursuers rising significantly to make up the gap in revenue and it has urged Parliament's justice committee to seek clarification from legal affairs minister Roseanna Cunningham about the impact of losses at its next evidence session tomorrow.
The Scottish Government believes cost-savings will result in the medium term, primarily in relation to judicial salaries as work is shifted from the Court of Session to the sheriff courts.
Details of a new fee structure with the intention "to move further towards full cost recovery levels" comes in a memo by Jan Marshall, deputy director of the Scottish Government's civil law and legal system division.
The Scottish Court Service recovers about 80% of the costs of civil litigation. "This approach implements the Scottish Government's policy objective that fees should cover the cost to public funds of providing court services," she says. "It is intended that the revised fee structure will set fees which are proportionate to the services provided to the court user and maintain affordable access to justice."
APIL warn that will inevitably mean higher court fees, as figures show that in 2012/13 the typical personal injury case generated £781 in fees for the Court of Session but just £270 in the sheriff court.
Ronnie Conway, Scottish co-ordinator of APIL said: "Rigorous parliamentary scrutiny has prompted the Government to admit that a new fee structure is to be introduced but it is still silent on how much sheriff court fees will need to be hiked to make up the shortfall.
"If vulnerable injured people and other court users are going to have to stump up the money to cover that cost, we need to be told."
The Law Society Of Scotland and the Faculty of Advocates has previously said the bill may restrict access to justice.
Which?, the consumer rights organisation, welcomed the Courts Reform Bill, saying it would improve access to justice. Presently, the cost of litigating in the Court of Session for lower value civil cases is "disproportionate and unfair to the public", said it executive director Richard Lloyd.
The Scottish Government says the move will free up the court to deal with the biggest cases. A spokeswoman said: "Under our court reforms we are introducing a new specialist personal injury court which is designed to provide a quick, efficient and effective route to justice at a more proportionate cost to litigants.
"As part of the implementation planning a new pricing table will be developed with specific fees set that are relevant to the provision of a specialist court - and we expect income levels will be largely maintained at current levels."
Among those giving evidence tomorrow is the Rt Hon Lord Gill, Lord President of the Court of Session, who undertook a review of the provision of civil justice.