The Scottish Liberal Democrats had tabled an amendment calling for reform of the system that the part said “continues to fail families and prevents lessons that could save lives being learned”.
MSPs blocked the amendment, which called for an independent expert review into whether Fatal Accident Inquiries should be removed from the remit of the Crown Office by 58 votes to 57 with six abstentions.
FAIs are a unique Scottish method of investigating the circumstances of deaths in custody and in major incidents such as disasters like the Glasgow bin lorry tragedy.
During the debate, Scottish Liberal Democrat justice spokesperson Liam McArthur said the system was “crying out for reform” and highlighted “scandalous” delays to cases.
He gave examples of two deaths which occurred a decade before their FAI investigation was completed.
Mr McArthur said: “It’s difficult to imagine the pain and frustration that loved ones must feel when such tragedy is followed by such a long silence.
"Scottish Liberal Democrats want a full independent review to consider if the FAI system should be removed as a Crown Office responsibility altogether.
“Assurances from the Scottish Government and the Lord Advocate, promises of extra funding to fix the problems, have simply failed to deliver the change that is required.
"In England, Wales and Northern Ireland, a distinct service handles such inquiries, an independent challenge function that keeps things moving.
"My amendment calls for the review to consider this and other options for kick-starting reform of the checks and balances in our justice system.”
Responding to the amendment, new justice secretary Keith Brown said internal reform was already underway and had resulted in reduction in wait times for investigations.
He said: “The Crown Office has, at the direction of the outgoing Lord Advocate, significantly reformed the arrangements for the investigation of deaths and applied significant additional resources to this work.
"These reforms have resulted in reductions in the duration of death investigations and it is expected that they will continue to do so.
"The full benefit needs to be allowed to work its way through the system, in my view, and the current Lord Advocate has welcomed engagement with justice spokespeople on this issue and I look forward to future engagement with his successor and I’m sure he or she, whoever is appointed, will undertake that engagement with people across the chamber.”
Instead of backing a review into fatal accident inquiries, Holyrood backed a Scottish Green amendment calling for more to be done around corporate and environmental crime.
Voting 93 votes to two, with 26 abstentions, the amendment calls for an acknowledgment of the “urgent need” to increase enforcement action against “corporate and environmental harm”.
Speaking prior to the debate, the Scottish Green justice spokesperson Maggie Chapman said: “This means empowering trade unions and giving regulators like the Scottish Environment Protection Agency greater enforcement powers.
"We should be encouraging sustainable business, not send a message that the most damaging behaviours are inconsequential.”