High Court Judge Pablo Ruz requested the PP hand over the laptops to help with the investigation into the party’s slush fund scandal.
The move could have proven key to ascertaining if disgraced ex-treasurer Luis Bárcenas carried out illegal handouts to party members.
But a study of the two hard drives on Thursday showed the contents from one of the laptops had been completely wiped out and the other may have been altered, Spanish newspaper El Mundo reported on Thursday.
Spain’s Popular Party has since admitted they reformatted the two laptops in April 2013 once Bárcenas had left the party.
They claim they were following "the common protocol for use and recycling of computer material" when previously used laptops are given to other party employees.
Bárcenas actually filed a complaint against the PP in March for forced entry into his office in the party headquarters in Madrid and the theft of two computers he stated were his.
The Popular Party alleged Bárcenas’s work space was not behind closed doors and that the two laptops, a Toshiba and a Mac, belonged to the party.
Police carried out an initial investigation but didn't take any further action.
Opposition party vice secretary general Elena Valenciano told a press conference on Friday that the normal procedure was "to format the disc, not to batter it".
Her comments were in response to the investigators’ claims that the hard drives' screws had been tampered with.