The document published by El Mundo newspaper fanned a scandal that has outraged Spaniards suffering in a recession and had sparked calls for Rajoy to resign earlier this year.
His ruling Popular Party hotly repeated its denials of any illegal payments to its members, while the opposition Socialists demanded Rajoy himself explain himself.
El Mundo published a page from what it said were original account ledgers showing payments to Rajoy and other party members in the late 1990s.
Today El Mundo published for the first time what it said was the front and back of a single, original page from the ledger, which it said dispelled doubts over whether it could have been fabricated.
It said the ledgers were compiled in part by the party's former treasurer Luis Barcenas, who is now behind bars facing corruption charges.
The party has distanced itself from Barcenas and has said it has no fear of possible revelations by him from his prison cell.
The excerpt purportedly showed extra payments to party officials including Rajoy when he was a minister in then prime minister Jose Maria Aznar's government in 1997, 1998 and 1999.
The entries include two payments to Rajoy of 2.1 million pesetas (12,600 euros/$16,200) in 1998.
The paper called the original documents a "smoking gun" in the scandal. It said the payments flouted a 1995 law barring such supplementary payments to members of the government.
All payments to party officials were properly declared, the party added.
"The PP denies making payments to people other than those included in their monthly salaries with the corresponding deductions for tax and social security," it said.
Barcenas, the former treasurer, was remanded in custody on June 27 as part of a far-reaching probe into political fraud and corruption.
Judge Pablo Ruz ordered Barcenas detained over allegations including money laundering and tax fraud, saying the move was aimed at preventing him from fleeing and to preserve evidence.
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