In his ruling — part of a long-running investigation into possible corruption by Spain's Popular Party (PP) — Judge Pablo Ruz said there was evidence the party had maintained "a certain current of money" for payments and receipts of funds.
He also said there were indications former Popular Party (PP) treasurer Luis Bárcenas and his wife had withdrawn some of this money and siphoned it off to accounts in Spain and Switzerland
Bárcenas and his wife will now appear in court on April 10th to answer questions in the matter.
The high profile corruption affair first kicked off in 2009 as a judicial investigation into alleged kickbacks involving members of the PP.
It exploded in January 2013 when Spain's El País newspaper published copies of account ledgers purportedly showing irregular payments from a secret slush fund to top party members, including Rajoy who has led the party since 2004 and took power in 2011.
The allegations come from the party's former treasurer, Luis Bárcenas, who has named Rajoy in the scandal.
Rajoy has repeatedly denied that he or other party figures received illegal payments and has said he will not step down over the affair but admitted when he was grilled in parliament over the affair that he had been wrong to trust Bárcenas.
In testimony in July, Bárcenas named Rajoy among Popular Party officials who benefited from the party slush fund, but Ruz said Rajoy would not be required to appear in court over the matter.
Conservative newspaper El Mundo calculated that Bárcenas paid a total of €343,700 ($456,000) to Rajoy over two decades.
Bárcenas was jailed in June 2013 pending an investigation into a separate corruption case, in which he is alleged to have held €47 million in secret Swiss bank accounts.