In the text conversation, the queen pledges her support for Javier Lopez Madrid - a close friend of the king - and calls him her "yoga mate".
The iMessage conversation, revealed by the online daily eldiario.es, dates back to October 2014. The businessman is among dozens accused of misusing bank funds for their personal use.
The scandal allegedly saw executives and board members at Caja Madrid and Bankia - the group whose near-collapse sparked an EU bailout of Spain's financial sector - use credit cards given out by the banks to spend some €12 million ($13 million) on themselves.
"I wrote to you when the story on the credit cards came out...," Letizia wrote in her message, according to El Diario.
"We know who you are and you know who we are. We know each other, like each other, respect each other. To hell with the rest. Kisses yoga mate (miss you!!!)"
Lopez then thanked her. "In future I will take extra precautions, we live in a very difficult country and I will be even more aware of my conduct." The king himself then joined the conversation, saying "We do indeed!"
The king has tried hard to clean up the royal family's image following a corruption scandal involving his sister that precipitated his father Juan Carlos's abdication in June 2014.
Last week, Princess Cristina gave evidence in a landmark corruption case centred on her husband's business dealings - the country's first royal to face criminal charges since the monarchy's 1975 restoration
The case has sullied the reputation of the monarchy and become a symbol of perceived corruption and greed among Spain's elites.
Spanish netizens on Wednesday revelled in the royals' embarrassment over the leaked conversation.
"Spain is a very difficult country," @ElPerricano tweeted above a photo of an old lady rummaging through rubbish juxtaposed to a shot of the royal family on a yacht.
The hashtag #CompiYogui - the term in Spanish used by Queen Letizia in her message of support and loosely translated as "yoga mate" - was the biggest trending topic on Twitter.
Many netizens jokingly used bears to illustrate their tweets in reference to the cartoon character Yogi Bear.
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"#CompiYogui attacking public money," @ulises_sevilla tweeted above a short segment of the scene of a bear attack in Oscar-winning film "The Revenant."
A spokesman for the royal palace, who refused to be named, told AFP the king and Lopez were no longer friends due to the businessman's judicial issues.
"The king doesn't directly explicitly support him (Lopez)," he added when asked about the messages themselves.
"It's different for the queen, who is clearer."