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Facebook logo is seen on a wall at a start-up companies gathering at Paris' Station F in Paris January 17, 2017.

Facebook told TechCrunch, which has email evidence showing messages that were deleted, that it retracted the messages "to protect our executives' communications" following the Sony Pictures email hack of 2014.

"Last month we decided that we should pause these discussions so can focus on other important work", the spokesperson told CNBC in a statement. "We did so in full compliance with our legal obligations to preserve messages", the company said. Interestingly, newer messages from Zuckerberg still remain in inboxes along with some conversations prior to 2014.

Facebook will begin alerting users whose private data may have been compromised in the Cambridge Analytica scandal starting April 9.

Trying to explain the discrepancy, a company spokesperson said Zuckerberg and other executives were using an encrypted version of Messenger, which included a "timer" that allowed them to have their messages automatically deleted.

But Zuckerberg's deleted messages didn't leave behind any such message, probably because they had already been read, many years ago.

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Sandberg said, "we always cared about privacy but couldn't balance it". The tampering wasn't publicly announced; and the users weren't individually informed, either.

Facebook has been using a secret tool to delete messages sent by its executives from the inboxes of their recipients, without disclosing the deletions to the recipients - or even recording that there was ever a message there in the first place.

Last month, a former employee of the United Kingdom consulting firm, Cambridge Analytics, accused the company of taking personal information from 270,000 Facebook users through a personality quiz - as well as the data of their friends. However, the timing of the announcement only comes after the company was caught deleting messages sent by CEO Mark Zuckerberg.

Facebook has come under intense scrutiny in recent weeks after news broke that Cambridge Analytica, a data firm with ties to President Donald Trump's campaign, may have had information on millions of Facebook users without their knowledge.

Deleting messages is not a function that Facebook offers to ordinary users, despite Facebook-owned WhatsApp and Instagram offering varying abilities to unsend messages. Codacons said just 57 Italians downloaded the Cambridge Analytica app, but that an estimated 214,000 Italians could be affected because the data mined extended to also the users' friends.