The UK government has added more countries from South America, Africa and England to their hotel quarantine list.
Portugal is one of those countries, meaning anyone who visits the country will have to spend 10 days in hotel quarantine after arriving back in the UK.
Fernandes will be part of the Portugal squad to face Azerbaijan, Serbia and Luxembourg at the back end of March.
But the Manchester Evening News says United could block Fernandes from linking up with his national team.
FIFA have handed domestic clubs power to make the decision on behalf of their players due to the coronavirus pandemic.
If Fernandes were to play for Portugal in the aforementioned games, he would miss United's fixtures against Brighton and Tottenham Hotspur.