Ministry officials on Tuesday said the number of applications filed on Monday was less than had been expected.
About half a million illegal immigrants holding Spanish work contracts and who have been living in the country for six months could, in theory, benefit from the one-off drive to grant legal status to illegal immigrants.
In a statement the ministry played down the lack of queues at social security bureaus, saying immigrants were not rushing to snap up their papers as they had three months to make applications and were taking heed of warnings from the authorities that incomplete applications would not be considered.
So it held out for an increase in numbers over the coming days.
Employers of the immigrants concerned are responsible for filing the applications and have until 7 May to do so. Bosses shirking the rules face stiff fines of $77,000 a day per employee employed on the sly.
In a statement on Tuesday Deputy Prime Minister Maria Teresa Fernandez de la Vega said that businesses and trades unions had acted responsibly in getting the scheme off the ground.
Half a million illegal migrants
could benefit from the plan
Immigrants must provide proof of their registration with a local council dating back to before 8 August last year, proof they have no criminal record and a six-month work contract.
With the Madrid government vowing to apply the new rules strictly, many of the immigrants facing the most difficult situations, like those from Africa who make the perilous journey to mainland Spain in rickety boats, could miss out on the plan for lack of papers.
The Spanish Commission for Refugee Aid (CEAR) has criticised the scheme for neglecting immigrants who had trouble getting necessary documents or simply did not have passports.