Brussels has suggested it prefers more targeted measures, rather than blanket bans.
Hungary's decision to re-introduce an entry ban on all foreigners from September 1, has ruffled feathers in Brussels.
Hungary will close its borders to non-residents from Tuesday to try and curb the increasing number of coronavirus cases, the government said on Friday.
The move comes as several European countries implement stricter COVID-19 measures.
The EU Commission reiterated that its more nuanced advice on COVID-19 related restrictions has been in place since July.
"There is the need to replace blanket restrictions to free movement by more targeted measures which are limited in time or in geographical scope, meaning, for example, that you apply restrictions to visitors from specific areas only," said Commission spokeswoman Vivian Loonela.
The Hungarian government defended its position saying that Hungary was a green zone while the rest of Europe was red.
"Maybe the border closure is just another provocation of the EU. Maybe Mr Orban should consider if he wants to be a member of the EU. If you are a member of a team, you play by the rules," Dutch MEP Sophie in' t Veld told Euronews.
Hungary was heavily criticised for not informing travellers and EU partners before the move which comes into force midnight tonight.
