Josie 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).
Dr Brash said her actions were "totally inappropriate" and he didn't know why she wasn't charged.
"The guy who threw mud at Gerry Brownlee has been charged but the woman who threw the dildo at Steve Joyce hasn't."
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 may 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 infamous 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.
Police would not comment on the specifics of the two cases.
But a spokesman said ethnicity or gender had "absolutely no relevance" to the process of deciding whether to lay charges.
In some cases, the spokesman said, police determined that a pre-charge warning was the most appropriate way of dealing with the matter.
"Police take into account a variety of factors, which are assessed on a case-by-case basis," the spokesman said.
"This includes consideration of the overall circumstances of the incident, the solicitor general's prosecution guidelines, the person's criminal history and their eligibility.
"Ethnicity or gender has absolutely no relevance to this process."
