Migrants are coming through Spanish enclaves Ceuta and Melilla and crossing the Gibraltar Strait in dinghies, the Spanish parliament heard.
As bodies continue to wash up on the shores of Spanish beaches, immigration policy is being reconsidered.
The minister wants all countries to agree to an improved registration system for everyone entering the EU.
Spanish politicians have insisted their country is providing a “warm welcome” to those descending on their shores.
According to government figures, 1,400 migrants resettled in the country so far in 2017 – short of the target.
But some NGOs have estimated this number is actually at 1,100.
Last week 160,000 marched in Barcelona to convince the government to take more migrants.
“In Catalonia, everything is ready to welcome them.”
Mr Zoido claimed it is time the EU worked closely with source countries like Morocco on prevention at the source, adequate control of borders an the fight against traffickers.