Dr Brash, a former National and Act Party leader and Reserve Bank Governor, said Ms Butler's actions were "totally inappropriate" and he didn't know why she wasn't charged.
Ms Butler, a nurse at Hillmorton Hospital in Christchurch, was not charged after she threw the dildo at Mr Joyce on Waitangi Day in protest against the Government signing the Trans-Pacific Partnership (TPP).
"The guy who threw mud at Gerry Brownlee has been charged but the woman who threw the dildo at Steve Joyce hasn't," Dr Brash said.
He said both acts were hugely inappropriate.
"Was she not charged because she was a woman or because she's Maori? I don't know, but she thought it was a huge joke and was delighted when she wasn't charged."
He said the only consolation was Kiwis who were opposed to the TPP might now be supporters due to her actions.
"Most people thought, 'Well, if that's what the people who opposed the TPP acted like, I'm in favour of the TPP after all'."
He said Ms Butler's action was not a good look for the country.
"Waitangi Day is a serious day for New Zealand. I understand she was there for the TPP but she seems to know nothing about it at all," he said.
Dr Brash has stirred up controversy with his comments on Maori in the past.
His now-famous Orewa speech in January 2004 attacked "race-based" policies and urged an end to what he saw as privileges for Maori.
The following month, Dr Brash was showered with mud thrown by a young protester inside a marae ground while attending a Waitangi event.
Police did not immediately comment on Dr Brash's latest comments.