UK Sport provides funding for the British ski team although the amount it has been giving has been gradually dwindling for more than a decade.
After Baxter's bronze medal at the Salt Lake City Olympics, the British Ski and Snowboard Federation was hoping for a much-needed funding boost.
"This could have serious repercussions for the British ski team, which would be a tragedy"
But after Baxter was stripped of his medal by the International Olympic Committee for testing positive for a banned substance, the BSSF is concerned the decision could affect the whole team.
Fiona McNeilly, BSSF operations director, told BBC Sport Online: "I hope UK Sport realises what Alain Baxter achieved.
"In my opinion he still finished third in the Olympic slalom.
"We have got a lot of good skiers in the British team and I hope they, and funding, don't suffer as a result of the IOC's appalling decision."
Former British skier Konrad Bartelski, now a BSSF board member, said it would be a travesty of justice if funding was affected.
He said: "The whole testing procedure is flawed when peope like Alain are penalised.
"This could have serious repercussions for the British ski team, which would be a tragedy."
McNeilly said she would be meeting with UK Sport bosses soon to discuss next season's grant.
Baxter is sponsored by drinks manufacturer Drambuie and Head and he has yet to hear if it will still fund him.
When he first returned home to Aviemore after the Olympics, Baxter had a number of lucrative offers.
He told BBC Sport Online: "I've not heard any news yet about all that but I hope my sponsors will continue to support me."