The outcry has reached the White House, with Polis fronting a media conference with Covid-19 expert Dr Anthony Fauci.
Polis said: "There's no way it's going to go to prisoners before it goes to people that haven't committed any crime. That's obvious."
Polis' U-turn then frustrated campaigners who pointed out prisons are the main source of large outbreaks in the state.
Denise Maes from the American Civil Liberties Union of Colorado said it was impossible to adhere to social distancing guidelines in prison.
Maes told KDVR: "There are many individuals in our jails who are frankly innocent. They are there pre-trial, simply because they cannot afford to pay bond.
"The notion that he's trying to demonise the individuals in those jails is really unfortunate."
Vaccinations across the US could start as early as next week, with the Food and Drug Administration speaking to Pfizer and Moderna over the next two weeks.
Colorado has had 239,000 Covid-19 cases and 3100 deaths.
More than 13.7 Americans have been infected and there have been more than 271,000 deaths.