Since its launch in November last year to 'promote mutual understanding between MSPs and business and related communities', the SPBE has faced claims it is being used as a vehicle for corporate lobbying.
Last month it was revealed that three-quarters of the first group to shadow MSPs on a SPBE scheme were lobbyists.
The CBI's call came as the Parliament's Standards Committee met to finalise a draft report on the scheme's future.
CBI Scotland head of media and public affairs Allan Hogarth said: 'It's important MSPs don't strangle this organisation to death. People may now think twice about using this scheme as its reputation is being damaged'.
The controversy began when Labour MSP Margaret Jamieson was asked to sign a confidentiality agreement by pharma giant Pfizer, with which she spent a 25-day secondment earlier this year.