The two-lane concrete flyovers were opened in 1970 as part of a £2.4m Mersey Tunnel relief scheme.
A Post Tension Site Investigation (PTSI) began in 2016 to assess the northern and southern sections, both of which are more than 240 metres in length.
This found several design and construction flaws, including drainage, internal support, barriers and bearings and recommended further intrusive investigations be carried out which requires a full closure.
The new survey will involve structural testing, removal of the road surface and drilling into the decks as well as underground assessments of every supporting column.
Inspection work is expected to take at least six months to complete becuase the flyovers have no access chambers to allow investigations.
Councillor James Noakes, Liverpool City Council’s Cabinet Member for Highways, said: “The Churchill Way fly-over is a unique design and over time that has led to some unique challenges which the council has been monitoring for the past few decades.
“This most recent survey we commissioned has now revealed certain elements of the structure cannot be guaranteed as safe – which given its age and past history is not surprising – and with any risk we cannot take any chances.
“Now we need to establish the severity of that risk and the only right and proper thing to do is to close the structure to allow engineers to carry out more detailed inspections.
“This is a complex process requiring numerous tests along the entire span and added to the fact there are no access chambers to assist the engineers it will take at least six months to do.
“Public safety is paramount and despite the obvious inconvenience this closure will cause to city centre commuters we cannot compromise on safety.
“As soon as this new survey is completed we will determine a plan of action and we will aim to keep all our city centre stakeholders and the public informed at every step.”