Liberal Democrats are to raise the issue and will demand ministers set up an independent commission to look at problems in policing.
It comes after Police Scotland lost some of its most senior staff.
Chief Constable Phil Gormley has been put on “special leave”, while one of his assistants has been suspended.
Meanwhile, a new chair has been installed at the SPA. Former Labour health minister Susan Deacon has replaced Andrew Flanagan, who quit after MSPs raised concerns over governance and transparency at the organisation.
The Liberal Democrat motion, to be debated this afternoon, states: “The Parliament does not have confidence in the structure of both Police Scotland and the Scottish Police Authority to deliver resilient and accountable policing at a strategic level.”
It goes on to make clear that it “believes that the Scottish Government should take responsibility for this”.
Liberal Democrat justice spokesman Liam McArthur said: “Police officers and staff work incredibly hard, day in day out, protecting our communities.
“I know many look on in disbelief at what is going on at the top. They have been left to make the best of a bad job following the SNP’s botched centralisation.”
Mr McArthur accused the SNP of having “bulldozed” the creation of Police Scotland, which was formed from eight regional forces in 2013, through the Parliament.
He said: “We have heard promises of a reset before. There is no escaping the fact, however, that the current policing structures are not fit for purpose.
“With a budget black hole, failing IT and a forced merger with the British Transport Police on the horizon, we need to see a fundamental change.
“Parliament has a legitimate role in setting out the structures of policing in Scotland. The SNP Government bulldozed through flawed proposals when it centralised the police.
“Having lost their majority, SNP ministers must now provide an opportunity for the damage to be undone with the help of an independent expert commission.”
However, Deputy Chief Constable Iain Livingstone, who is in charge of day-to-day policing, said he had “absolute confidence” in Police Scotland’s staff and leadership.
He told Scotland on Sunday that he wanted Police Scotland to be free of political interference and return to being an “apolitical” service.
“This is clearly a challenging time for policing in Scotland and my focus continues to be on meeting the operational and organisational challenges we face, and providing the leadership of policing that the people of Scotland rightly expect,” he said.
Mr Livingstone added: “Leadership exists across all aspects of policing from my role as the Deputy Chief Constable all the way through the organisation to the Police Constables serving their local communities.
“I have absolute confidence in the leadership provided by all the officers and staff that serve in Police Scotland and the qualities, skills and experience that we collectively possess.”
Meanwhile, Ms Deacon said she would be working with the board of the SPA, Police Scotland and others “to accelerate improvement, and to build trust and confidence in policing”.
She said: “This approach is one part of helping to turn the SPA outwards to the people and interests it is there to serve. That’s an approach I want to develop further around our next public meeting of the authority on December 19.”
A Scottish Government spokeswoman said: “Scotland is a safer country now than a decade ago - with less crime, including lower re-offending rates and fewer incidents of violence, and stronger criminal laws in place to enable our police and prosecutors tackle crimes such as sex offending and human trafficking.
“Scotland’s unified police service has been key to much of this progress, with reforms helping to protect frontline policing during a period of constrained budgets, while ensuring that local officers have better access to a range of national, specialist resources in key areas of crime investigation and prevention.
“We welcome the recent appointment of Susan Deacon as Chair of the SPA and encourage all partners to engage constructively with her efforts to further strengthen Scottish policing.”