Alex Salmond earlier assured MSPs the external inquiry had fully investigated the issues highlighted by psychiatrist Dr Jane Hamilton about the running of the Mother and Baby Unit at St John's Hospital in Livingston.
However, documents obtained under freedom of information legislation found that, while those conducting the investigation looked at "specific" criticisms, they did not look in detail at the full period covering the allegations.
Health Secretary Alex Neil and NHS Lothian have also stressed it was an external inquiry but internal papers show Dr Margaret Oates, a consultant psychiatrist for Nottinghamshire Healthcare, who wrote the report, had been involved in two previous reviews of the unit, generally concluding there was no serious problem.
Scottish Labour's health spokesman Neil Findlay said: "These documents show Alex Neil should not have simply accepted assurances from NHS Lothian that the inquiry into Dr Hamilton's complaints was as exhaustive or as independent as they claimed. Alex Salmond then echoed those assurances during First Minister's questions last month.
"Three crucial years in this sorry tale appear never to have been examined in detail and the supposed independent inquiry was undertaken by someone who had previously reviewed the unit and given it a positive assessment.
"This seems inappropriate given the seriousness of the allegations and the concerns raised by Dr Hamilton."
Dr Hamilton was appointed to run the unit in 2007. Before the end of that year she raised concerns over how the unit was being run and shortly afterwards warned in writing that patients could die. Two women subsequently took their own lives and the family of one is now suing the health board for medical negligence.
Dr Hamilton also complained about being bullied and victimised. Late in 2008 she herself was the subject of a complaint by a colleague. This was investigated in 2009, during which time Dr Hamilton was off work with stress-related illness.
Although her defence organisation the Medical Protection Society rejected the complaint against her as unfounded and retaliatory, Dr Hamilton did not return to her job.
She recently turned down a six-figure settlement as it was conditional on her withdrawing and never repeating her complaints.
In 2012 NHS Lothian ordered an "external independent" inquiry into the unit and Dr Hamilton's concerns.
The report, written by Dr Oates, said: "We feel it is outside of our remit to go back and assess the validity or otherwise of the accusations and counter-accusations and the possible reasons for them between 2007 and 2009.
"Our remit was only to assess the safety and functioning of the service currently (in 2012) and in the recent past."
Internal documents also show that in 2008 there was a review of the MBU by the Quality Network for Perinatal Mental Health Services, of which Dr Oates was director.
A second psychiatrist involved in this review also took part in the one in 2012.
Dr Oates also headed the inquiry into the MBU's handling of the death of Claire Donald, who took her own life in January 2011.
There are no questions over Dr Oates's probity but Mr Findlay expressed concern that her previous associations with the MBU had not been made clear.
Dr Oates previously told The Herald she did not want to comment further but that her 2012 inquiry did address Dr Hamilton's concerns that related to the "current functioning" of the MBU.
A Scottish Government spokeswoman and Dr David Farquharson, Medical Director, NHS Lothian, said the unit had been investigated by a review group that was both independent of NHS Lothian and the Scottish Government. These experts had noted their satisfaction with the level of specialist knowledge and skills of clinicians and the standard and quality of care. Dr Farquharson said Dr Hamilton's allegations had been investigated.
The Scottish Government said the unit became one of only two in the UK to be awarded a rating of excellence by the Royal College of Psychiatrists in 2013.