They are asking that the European Commission amends its own legislation so that ISA and another fish disease, VHS, can be added to a list of diseases qualifying for financial aid.
The Scottish Parliament's European Committee is asking for assurances that all possible avenues for financial assistance have been explored.
A report from the committee on the effects of Infectious Salmon Anaemia (ISA) says the disease has cost £100m and 200 jobs in Scotland.
MSPs are also urging Brussels to explain why salmon from Norway - which does not does not have to follow EU fish farming controls - is allowed to be sold in Europe.
They are asking that the European Commission amends its own legislation so that ISA and another fish disease, VHS, can be added to a list of diseases qualifying for financial aid.
Maureen Macmillan, Labour MSP for Highlands and Islands region, said: "Our committee believes that money could possibly be available from EC structural funds which would require pound-for-pound match funding by the Scottish Executive.
"We are asking the executive to give us its absolute reassurance that all possible avenues of (European) Community financial support have been explored under the FIFG (financial instrument for fisheries guidance)."
The Scottish Executive is being asked to consider the regime on farms suspected of having ISA.
Insurance scheme
The committee also suggests a joint insurance scheme and ways of helping fish processors move towards other ways of dealing with the problem.
Since the disease was first recorded in Scotland in May 1998 at a farm in Loch Nevis, there have been 11 confirmed cases at fish farms and 14 suspected outbreaks.
EU rules required tough measures to control the disease, which led to a "crisis of confidence" within the industry in Scotland, said the report.
The industry says it has been badly affected by the policy of publicly naming farms that were merely suspected of having the disease.