Labour warned the proposals would allow the Scottish Government to "shut down schools and confine people to their homes at the drop of a hat".
The Coronavirus (Recovery and Reform) (Scotland) Bill would give ministers the ability to respond to public health emergencies in a similar way to legislation passed in the wake of Covid.
This includes imposing lockdown restrictions, allowing court hearings to take place remotely and restricting access to schools.
The Government said the move would maintain provisions that enable ministers “to enact measures via public health regulations for any future public health threats, bringing Scotland into line with England and Wales”.
But both Labour and the Tories have branded it a "power grab".
Writing on Twitter, Mr Neil said he agreed "no government should get such draconian powers other than in very exceptional circumstances and only with explicit parliamentary approval".
Mr Neil was health secretary from 2012 to 2014 and social justice, communities and pensioners' rights secretary from 2014 to 2016.
Murdo Fraser, Scottish Conservative spokesman for Covid recovery, said: “The SNP’s plans to retain Covid powers are facing condemnation across the political divide – and Alex Neil is right to stand up to his party over this blatant power grab.
“Such extensive powers should only ever be granted temporarily, in emergency circumstances.
“Anyone who wants a fair, accountable and democratic government should be appalled by these proposals, regardless of their political position.
“If the SNP won’t listen to the 85 per cent of Scots who are opposed to these powers, they should heed the words of their own political grandee, and row back on this unacceptable overreach.”
Deputy First Minister John Swinney previously said the Scottish Government had "already removed many of the temporary measures that supported our response to the pandemic, which are no longer needed".
He said: “However, we believe those pragmatic reforms that have delivered demonstrable benefit to the people of Scotland should continue."