The reporter by Professor Campbell Gemmell, former head of the Scottish Environment Protection Agency, called for 'urgent' action to protect at-risk species after Brexit.
He called for a dedicated court and commissioner to safeguard Scotland's world-renowned environment once EU protections disappear.
Warnings last years said some of the rarest species in Scotland face being lost unless laws are brought in to secure vital conservation work.
The Scottish Environment LINK, a coalition of more than 35 charities said red squirrel, some birds of prey and certain sea mammals are vulnerable.
And they remain concerned not enough is being done to ensure post-Brexit environmental protections are created.
Mr Gemmell's report, for the conservation groups, said: "What we stand to lose is serious and must be addressed and that serious reform of our governance arrangements is necessary with or without the UK's EU withdrawal and its consequences for Scotland".
Mr Gemmell, a professor of environmental policy, regulation and governance at the University of Glasgow, suggested creating a post for a commissioner for the environment, as well as a dedicated court.
The report states: "For the functions being lost to Scotland by the UK's withdrawal from the EU and the resultant gaps in oversight, application of powers of the Commission and the Court of Justice of the European Union and expert knowledge exchange dimensions of the EU institutions and fellow member states, it is clear and ought to be publicly stated and agreed that existing arrangements at the Scottish and UK level are inadequate."
The UK Government has published a wide-ranging Environment Bill for England.
It pledges to set targets to reduce plastic pollution, improve air and water quality, and creates a new Office for Environmental Protection.
But environmental groups are concerned that, with 80 per cent of environmental protections stemming from EU laws, ministers in Scotland have not yet made similar moves.
Deborah Long, LINK's chief officer, said: "Scotland is internationally recognised for its environment, land and seascapes.
"We rely on EU laws to enforce the strong environmental protections we have in place in Scotland and these are at risk from Brexit.
"Despite the chaos of politics today, we must ensure we can tackle today's climate emergency and nature crisis through effective laws.
"We urge the Scottish Government to embed the protections our environment needs into Scottish law now and in the event of whatever may happen with Brexit."
Environment Secretary Roseanna Cunningham said: "The Scottish Government is committed to maintaining or exceeding EU environmental standards despite the uncertainty posed by
Brexit and has acted to ensure our environmental laws and regulatory systems are robust.
"We published the analysis report on our consultation for future principles and governance earlier this month and are carefully considering the results as we work to put in place alternative governance procedures for the environment, as outlined in the Programme for Government.
"We will put in place interim, non-legislative measures in the event of a no-deal Brexit to ensure that current standards do not slip while we develop longer-term solutions.
"Our approach will ensure we remain true to the EU environmental principles."