Spanish Prime Minister Pedro Sanchez said the British Government's decision to remove Spain from its safe countries list was not justified.
Mr Sanchez said the move to introduce a two week quarantine for people travelling from the country to the UK was unfair.
He added that the Spanish Government was currently in discussions with Britain to see if changes could be made to the new quarantine rules.
Mr Sanchez said it was an "error" for the UK to have considered the rate of coronavirus infection in Spain as a whole when most regions had a lower Covid-19 rate than in Britain.
However Health Minister Lord Bethell has explained it would be too "challenging" to introduce a regional exemption list.
“Within individual countries there is no way for us to control intra-country transport, it is therefore very difficult and challenging to have a regional exemption list, and that is why we’ve not been able to give exemptions to the Balearics," he said.
It comes after holidaymakers also called on the British Government to take a more "targeted" approach to the quarantine rules.
But on Monday evening the Foreign Office updated its travel guidance to warn against all but essential travel to the Balearic and Canary Islands, as well as mainland Spain.
Downing Street warned “no travel is risk-free” after a coronavirus quarantine requirement for people arriving in the UK from Spain was reintroduced.
The Prime Minister’s official spokesman said decisions on border measures and travel advice “can be changed rapidly if necessary to help stop the spread of the disease”.
He said: “Unfortunately no travel is risk-free during this pandemic and disruption is possible and so anyone travelling abroad should be aware that our travel advice and exemption list is under constant review as we monitor the international situation.”
Airlines TUI and Jet2 announced they were cancelling all flights and holidays to Balearic Islands and Canary Islands after the FCO's updated its travel advice.
