The FSA fears advisers and employee benefit consultants will switch group personal pensions (GPP) around the market to continue receiving commission.
Head of investment policy Peter Smith warned he had "heard rumour and anecdote" in the individual markets for GPPs that people were thinking of ways of moving products around so they continue to be paid commission.
Smith said: "We can see the current market is driven by commission to some extent and there is clearly an incentive for people who want to get commission to find ways of doing it.
"There are people out there thinking about how they can do this because they see a possibility of continuing to be paid commission.
"Given that one of the issues we are trying to address is commission bias we think there is a real problem here we need to address."
On Tuesday the FSA issued proposals for removing commission bias from the GPP market by ensuring that employers will be able to agree up-front how much investment advice will cost them and how they will pay for it.
The FSA acknowledged the possibility of market participants avoiding any new rules the FSA might make for GPPs by turning instead to market offerings based on occupational pension schemes.
However, it said it was not necessary at this stage to investigate extending its regulatory scope, but will revisit this if the market should develop along occupational scheme lines.
Smith said regulation of trust-based schemes remained the responsibility of The Pensions Regulator but added the two bodies will continue to work together.
He said: "We don't see the need to extend our scope TPR is active in this area and we would expect that to continue. We are very much in dialogue with them to make sure our respective roles are clear to market participants. Within our existing remits we can do things to head off potential abuse."
The Pensions Regulator said: "This is an important issue for the regulator and we support the aims of these proposals. We will continue to work closely with the FSA to reduce the potential for regulatory arbitrage.
"At this time our focus is on further developing our understanding of how this may affect the behaviour of advisers, providers and other interest parties."
Scottish Life group head of communications Alasdair Buchanan said he was pleased that FSA had made it clear that there should be no regulatory arbitrage available between contract-based and trust-based arrangements.
He said: "Any providers, or advisers, who thought there would be an opportunity to continue with a traditional initial commission approach, by enabling or recommending switches to trust-based arrangements, will now have to think again."
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