The European and external relations committee highlighted "significant discrepancies" in how Whitehall departments handle devolved interests in relation to the UK agenda.
They called on Scottish ministers to encourage London departments to "adopt a standardised and consistent approach based on best practice".
The committee looked at the impact of the Treaty of Lisbon, which came in last December.
MSPs said it provided the potential for a "substantially increased role" for Holyrood.
But their report also said: "Given the significance of areas like freedom, security and justice for Scotland, there is a need for improved mechanisms to safeguard the Scottish position in any negotiations with the EU and to deal with conflict resolution within the UK."