In its budget plan and report, published this morning, the organisation forecasted that it would have to deal with even more cases relating to pensions and, particularly Sipps, than it has this year.
The FSCS predicted it would receive at least 5,407 Sipp claims in 2015/16, compared with 4,958 expected in 2014/15. The report stated this could be even higher.
It said: "This (the expected 5,407 Sipp claims for next year) is a provisional forecast based on current expectations, and it is possible that claims could increase above these levels."
The report said: "FSCS has seen increasing numbers of claims against independent financial advisors in relation to life and pensions advice.
"In particular, we are seeing claims in relation to advice given to transfer funds from existing pension schemes to Sipps. In many cases the Sipp fund was then invested in risky, non-standard asset classes, many of which have become illiquid.
"FSCS's experience of these claims is consistent with warnings published by the FCA in relation to Sipps and the conduct of some firms.
"We expect this trend to continue and there is considerable uncertainty as to the amount of compensation we may have to pay in relation to these claims."
It warned that the forecast compensation costs could also "materially increase, particularly in the event that FSCS compensation payments include investment losses resulting from pensions advice received by investors".
The report stated: "This could have a significant impact on the costs falling to life and pensions intermediaries. FSCS will keep claimants and levy payers updated on developments with implications for the levy."