The Catalan giants recently went public on their views of the standard of Spanish refereeing, with club president Sandro Rosell blaming match officials for hindering his side throughout the season.
Jose Callejon then criticized Barcelona for contradicting themselves in their statements about referees, but Guardiola remains adamant that they deserve the right to voice out their unhappiness.
"Barca do not complain about referees," the 41-year-old said.
"But a different thing is to say if in this or that situation we could have been awarded a penalty.
"If that is complaining, then we complain. The only thing I know is that we do not help referees and we do not to them any favours.
"I get annoyed when referees make mistakes which damage us, but then I think: 'They made a mistake'.
"I represent a club and I know that tomorrow, in another decision, maybe they will favour us. And I have to live with it.
"If we are defeated, we have to do better. And I know this, having spent so many years at this club."
Guardiola went on to address Barcelona's seven point gap from current league leaders Madrid, declaring that the defending champions are still in the race.
"I want everyone to know that we will do everything possible to win every title, that they feel that we will try it," he assured.
The 2011 FIFA World Coach of the Year recipient also played down rumours that he is nearing the decision to extend his contract as manager, which expires at the end of the season.
"I am very thankful for the support of the president and the board, but I am the one who has to decide about the renewal," Guardiola explained.
"When I have done it, the president will be the first to know."