"Among other lines of action, the police force has drawn up an action plan against possible nuclear, chemical or biological terrorist attacks," Alonso said on Cadena Ser radio.
"To date, we have no concrete indication of any such activity under way," said Alonso, adding that the work of the 1,682 newly-assigned agents was mainly preventive.
Alonso was reacting to a report in the ABC daily announcing the new focus for the security agents under a defence plan which the paper said was based on the premise that "Islamic terrorism represents a permanent and global threat."
The budget for the defence plan is 2.5 million euros (three million dollars), the paper said.
Last week, the interior ministry announced it was stepping up police recruitment and hiring 347 extra officers to crack down on Islamic extremists following the March 11 train bombings in Madrid.
To date Spain has 74 officers specially trained to counter Islamic extremists. The majority of those detained over the March bombings which killed 191 people in the country's worst ever terrorist attack are Moroccans.