The UNHCR has backed the creation of an EU burden-sharing mechanism for illegal immigrants but has so far failed to take a position on the proposal to set up joint reception facilities in Libya to process asylum applications.
At the same time it warned that burden sharing should not be "a substitute for state responsibility", and that member states should do more to help asylum seekers.
The declaration is contained in a letter from the United Nations High Commissioner for Refugees, Antonio Guterres, to the EU Czech Presidency, a day before EU interior ministers meet in Luxembourg to discuss urgent European Commission proposals designed to help Malta and Italy fight illegal immigration.
Mr Guterres said that, while the UNHCR supports increased measures to help the EU's over-burdened member states and Libya, "EU members should ensure that migration control measures do not undermine fundamental rights of asylum seekers and refugees.
"UNHCR is prepared to support responsibility-sharing mechanisms within the EU, including some relocation of people found in need of international protection, when reception and asylum systems in specific member states are under strain.
"At the same time it is important for EU member states to redouble their efforts to improve asylum facilities and procedures, as part of the effort to build a Common European Asylum System," Mr Guterres wrote.
Referring specifically to Libya, considered as the main transit point of departure for thousands of illegal immigrants heading for Europe, the UNHCR chief said that he fully supports the EU's initiatives to help that country improve the general conditions for asylum seekers and refugees.
At the same time he appealed to EU member states to admit those who appear to be in need of international protection.
Italy recently drew the wrath of the UNHCR when it adopted a policy of sending would-be immigrants back to Libya without giving them a chance to apply for asylum. The policy has been welcomed by Malta which says it will deter human trafficking.
Libya is asking the EU for $1 billion worth of equipment and training in exchange for more support on the illegal immigration issue. The EU is still evaluating this request but has already stated that it is willing to support Libya and cooperate with Tripoli to stem the flow of illegal immigrants towards Europe.
One of the proposals which the Commission will be discussing with interior ministers tomorrow is to open reception facilities in Libya and other north African countries, jointly with the UNHCR, in order to assess asylum applications without the need for aspiring refugees to cross the Mediterranean.
But the UNHCR chief did not take a position over this proposal and avoided any reference to it in his letter to the EU Presidency.
The package of measures to be discussed by EU ministers also includes more financing for over-burdened member states like Malta and Italy, the reinforcement of EU patrols and the holding of a conference with Libya, as President of the African Union, aimed at coming up with joint solutions.