Bartomeu was a vice president under former president Sandro Rosell when Neymar was signed in 2013 and he the club have been accused of defrauding the tax office of 2.8 million euros (2.08 million pounds) in 2014.
Rosell, who has also denied wrongdoing, resigned over allegations the club did not pay several millions more in taxes it owed for 2011, 2012 and 2013, saying he wanted to protect the club's image.
"In the evidence given in front of the judge Pablo Ruz, president Bartomeu gave explanations to all about which he was questioned," Barca said on their website (www.fcbarcelona.es).
"In particular, he defended the decisions taken in the matter, always in consultation with the club’s financial advisers," they added.
"He made it clear that it has never been his intention, nor that of the club’s executives, to aim to defraud the National Tax Office."
The tax probe was launched after a member questioned the figures given by the club for the Neymar deal. Barca initially said they paid 57.1 million euros ($65.16 million) but later admitted the cost was nearer 100 million.
(Reporting by Iain Rogers, editing by Pritha Sarkar)
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