However, the New York Times has reported, citing sources familiar with the matter, the social media giant intends to unify the trio of applications.
Such a change was claimed to mean a user on WhatsApp could send a message to someone on Facebook Messenger seamlessly.
However, it was clarified each piece of software would remain accessible in a standalone fashion.
The outlet also insisted Zuckerberg has insisted the three apps should all boast end-to-end encryption in order to protect user privacy.
Commenting on the decision, Facebook declared it wanted to “build the best messaging experiences we can; and people want messaging to be fast, simple, reliable and private.”
The firm went on: “We’re working on making more of our messaging products end-to-end encrypted and considering ways to make it easier to reach friends and family across networks.”
It was also noted Mr Zuckerberg hopes to increase the likelihood of users remaining “engaged” in Facebook-owned software as part of a bid to prevent people from using competing services from tech rivals such as Google and Apple.
The move to integrate the services appears to stray from promises both WhatsApp and Instagram would retain some distance from Facebook when the two were acquired in their respective years.
The growth of both Instagram and WhatsApp was said to be part of the reason for the change in stance, the New York Times added.
Facebook was now said to believe closer integration will benefit the firm’s “family of apps”.
It is understood in order to complete the process, Facebook staff are having to “reconfigure” how Messenger, WhatsApp and Instagram’s chatting clients work on a fundamental basis.
It was emphasised Facebook is in the “early stages” of the move but it plans to complete such changes by either the end of this year or the start of 2020.
Facebook has admitted there is still much “discussion and debate” regarding the integration.
The social media giant said: “As you would expect, there is a lot of discussion and debate as we begin the long process of figuring out all the details of how this will work.”