Representatives for the Zambian artist confirmed the move on Wednesday, two days after Melbourne rock outfit King Gizzard and the Lizard Wizard announced it was also withdrawing.
Sampa The Great was announced as part of Bluesfest's extended line-up along with controversial Sydney-formed indie rock band Sticky Fingers.
"We started contact with Bluesfest to inform them of our standpoint within half an hour of receiving the embargoed press release and seeing the remainder of the line-up," Sampa's representative said in a statement.
"We then delivered final confirmation to Bluesfest at 7:36pm AEDT on Tuesday 14 February that Sampa was coming off the line-up, in the hopes they would remove her from all materials before they announced the following day."
Bluesfest did not comment on Wednesday but emailed ticketholders on the back of festival director Peter Noble defence of Sticky Fingers' inclusion in the line-up.
"Please take the time to educate yourself with the facts regarding Sticky Fingers," Mr Moble wrote in the email.
"They aren't monsters; they are a seriously great Australian band who singers has had to overcome barriers that would hae sidelined all but the most determined to continue to perform."
Mr Noble questioned why there was such an ongoing witch-hunt toward a man with a mental health disorder.
"A man who is attempting to grow and function in society.
"Shouldn't we forgive and provide a path to redemption for artists who have taken ownership of their situation and have proven for many years now that they have found a way to function responsibly?"
Sampa The Great on February 15 detailed her first Australian shows of the year at A Festival Called PANAMA in Tasmania, WOMADelaide at Adelaide's Botanic Park, and Ability Fest at Melbourne.
Returning to Australia to play WOMAD and Panama with her Zambian band was extremely exciting for Sampa, her representative said.
"Ability Fest is a new one for Sampa and playing in Naarm is always special. This one will be even more so, given how accessible it is," they said.
"Sampa, her band, and the crew's safety is always our main priority, and we feel confident these festivals can provide that."
The six-piece rock band King Gizzard and the Lizard Wizard on Monday announced on social media it was cancelling its Bluesfest appearance, saying it stood against misogyny, racism, transphobia and violence.
"Surprised and saddened to see Bluesfest commit to presenting content that is in complete opposition to these values," the band wrote.
"We are deeply disappointed to be in this position but sometimes you need to be willing to make sacrifices to stand up for your values."
Controversy has surrounded Frost's behaviour, with Indigenous Australian singer-songwriter Thelma Plum in 2016 accusing him of threatening behaviour towards her, for which he later apologised.
The band later announced a hiatus from 2017, with Frost revealing he was diagnosed with bipolar schizophrenia and would be attending rehabilitation and therapy.
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