The late scratching of all but four horses from the 2014 Ballarat Pacing Cup is under investigation by Victoria's Racing Integrity Commissioner.

Six of the ten runners were scratched after stewards discovered the use of over-sized sulkies.

The investigation will focus on how and when the non-compliant sulkies arrived in Victoria, when Harness Racing Victoria became aware of the problem, and their response.

It will also consider whether the horses should have been permitted to race with alternate sulkies, or under a warning that non-compliant sulkies would not be tolerated in the future.

"All parties involved have accepted that the situation at the Ballarat Pacing Cup was handled poorly," Minister for Racing Martin Pakula said in a statement on Thursday.

"This investigation will ensure that the issues are addressed immediately for the benefit of the harness racing industry and all involved."

A report will be handed to the minister by March 2015.