In a top-level Popular Party meeting held behind closed doors, Rajoy told the party executive that corruption was a thing of the past in Spain.
Without specifically mentioning the high profile corruption case involving former Popular Party treasurer Luis Bárcenas, Rajoy said: "I don´t want Spain to become an uninhabitable country because people are accused without evidence."
"This has nothing to do with hiding anything, or trivializing or forgetting. It's about acting sensibly," El Pais quoted the prime minister as saying on Wednesday morning.
"All corruption is unacceptable and we need to fight it wherever it appears," quoted El Mundo newspaper.
"This party has acted as soon as it learned of (any corruption) at a level that no one else has equalled, and we will work together with the justice authorities and used all methods to fight corruption," the prime minister said.
Rajoy also made a direct reference to what he called incidents of "harassment and verbal intimidation" that various members of his party had experienced in recent times.
In an indirect reference to the form of protest known as the "escrache" in which protestors target individual politicians at their home or place of work, Rajoy described this behaviour as unacceptable.
The Spanish prime minster also said this form of protest was not acceptable to most Spanish people.
In his speech, Rajoy was also keen to stress that next year would be better for Spain.
"In 2014 Spain will show clear signs of growth and we will start to create employment."
He said the process would be difficult but noted: "Spaniards will see tangible results of the efforts we have made."
Rajoy stressed that the economic growth and the creation of jobs remained his first priority. He also said that "neither I nor anybody else in their right mind can be satisfied with labour reform (in Spain)".
The Spanish prime minister went on to talk up his government's economic performance.
"We have lowered the public deficit, and our public deficit and we avoided a rescue.
He said there was"positive economic data" which suggested the country could turn the corner.
El País also quoted the Spanish leader as saying a successful budget had led to improvement in public administration. "The state is functioning and public services are guaranteed," Rajoy stressed.
El País also said that such a meeting of the Popular Party's executive — the first in nine months — was usually be a low-key affair. However, the event was given extra importance because Spain's ruling party have generally maintained public silence since the corruption case involving their ex-treasurer erupted in January.