Manuel Morocho, chief inspector of Spain’s Unit of Economic and Financial Crimes (UDEF), claims the People’s Party (PP) acted as a “criminal organisation” in accepting payments from a slush fund.
He also claims there is “circumstantial” evidence to link Mr Rajoy to the criminal activity.
The corruption scandal has been ongoing for months after Mr Rajoy achieved the dubious accolade of being the first sitting Prime Minister to testify as a witness in a criminal trial.
The PP allegedly used a parallel system of accounts to siphon bribes into party funds through “box B”, handled by former party treasurer Luís Barcenas, among others.
Appearing before a Spanish Congressional commission investigating the matter, Mr Morocho described the network as totally corrupt in his damning evidence.
He said: “An organisation that has operated for a long time, which has penetrated to very deep levels in public administrations until it has become parasitic and absorbed the capacity of a political leader to allocate and manage public funds…
“That is the concept of corruption in its purest form.”
The criminal investigator said Mr Rajoy would have benefitted from the payments “indirectly”.
According to Mr Morocho, “circumstantial” evidence also connects Mr Rajoy himself to the payments, as well as former Spanish ambassador to the UK Federico Trillo.
Former PP treasurer Mr Barcenas has admitted he regularly handed over envelopes of black money to politicians from his party.
Mr Rajoy is included in Mr Barcenas’ notes, however Mr Rajoy is not being prosecuted in the case and there is no concrete evidence he was handed money.
Mr Barcenas says any suggestion he was involved in the bribes is “absolutely false” as at the time of the payments he was in charge of the policy, not the financing, of the PP.
The inquiry into PP finances has been running for more than a decade, and Mr Morocho told the commission the UDEF had been pressured to stop its investigation.
A number of those implicated in the case reportedly complained to UDEF about the investigation.
Opposition party Podemos blasted Mr Rajoy’s party over attempts to “intimidate” the independent investigators.
The investigation has resumed following a four-month break.
Mr Morocho’s comments could not come at a worse time for embattled Mr Rajoy, who is facing a huge backlash to his handling of the Catalan independence crisis.
Having imposed direct rule on Catalonia, he is now set to hold “free and democratic” elections after dissolving its government.
But the corruption allegations remain near the top of the agenda in Spanish politics.