The Spanish government estimates that 10,000 migrant minors are alone on Spanish soil without their parents.
It comes as funding of €40m was made available for regions willing to welcome them.
The new Socialist government, in power for three months, has taken this "exceptional initiative" faced with a "rise in the number of arrivals over the past few months," it said in a statement.
This morning, 49 apparent minors from northern Africa arrived on a beach in the southern city of Tarifa on board makeshift boats, the central government's representative office in the Andalusia region said.
The government has set aside "a budget of €40 million (to be distributed) among regions to welcome unaccompanied foreign minors," the ministry said.
Health Minister Carmen Monton said there were currently 10,000 such minors in Spain.
In April, Spain's previous conservative government had counted just over 6,200 unaccompanied minor migrants, compared to 4,000 in 2016.
Many of these children and teenagers come from Morocco.
They are put under the protection of the regions or cities where they arrive, mainly the southern region of Andalusia and the overseas territories of Ceuta and Melilla in northern Africa.
The government wants to incentivise other regions to take charge of some of them. By law, minors cannot be sent back to their country.
When they reach 18, they are entitled to Spanish nationality if they have been in a centre for at least two years.
But there has been criticism of the way Spain welcomes unaccompanied foreign minors, particularly in Melilla, where many sleep in the streets or in caves waiting to smuggle themselves onto a boat to mainland Europe.
In Ceuta, local government spokesman Jacob Hachuel recently said the minors should be returned to Morocco, saying they were better off among their own families.
Meanwhile, Cyprus has appealed to the European Union to offer it more help with illegal migrants, warning it would be unable to cope if the influx of arrivals continues to its shores.
The government held an emergency ministerial meeting to address the issue after more than 140 migrants reached the island in the past four days alone.
"There will be a round of contacts with our European counterparts, especially from Mediterranean countries, facing the same problem, so there is better coordination of actions at European level where we demand European solidarity," said Cypriot Interior Minister Constantinos Petrides.
He said EU immigration policy should not place a "disproportionate burden" on front-line states or small members like Cyprus "that cannot develop structures ... to absorb these flows".
Cyprus, in proportion to its population, says it faces one of the most serious problems of migratory flows compared with other countries.
Cyprus had received 4,022 asylum requests in the first eight months of 2018, which was 55% more than for the same period last year, Minister Petrides said.
Among other measures, Cypriot ministers agreed to step up sea patrols, enforce repatriation agreements and speed up the asylum process to make sure the non-entitled get sent back.
On the other hand, it will be made easier for asylum applicants to find work.
The UN refugee agency has estimated that at least 2,000 migrants came to Cyprus since 2015.
