The guidelines were developed over four years for the healthcare profession on how to provide safe and lawful abortion services within existing laws.
But religious leaders said they were not consulted.
Earlier this week, the Catholic archbishop of Lagos was quoted as saying that the guidelines would legalize abortion through the backdoor.
On Thursday, Governor Babajide Sanwo-Olu said further sensitization of the public and stakeholders was needed to ensure a clearer understanding of the guidelines.
Lagos state law allows for the therapeutic termination of a pregnancy – this means medical professionals can terminate a pregnancy where the life of the mother is in danger or the foetus’ chances of survival are considered minimal.