The three services will, however, continue as stand-alone apps, the report said, citing four people involved in the effort. With a merged platforms, an Instagram user could send a private message to a WhatsApp user, a process not now available.
Whatever the reasons, the process is likely to take its time, with the New York Times suggesting that Facebook is in the early stages of the process, and that it will likely complete the integration by the end of this year, or by early 2020. They will need to change how the apps function at their most basic levels.
Zuckerberg also wants to have all three platforms to feature end-to-end encryption, so any message you send to whichever platform will be secure.
WhatsApp already uses end-to-end encryption but, apparently, the integrated services will all use it.
It added: "We're working on making more of our messaging products end-to-end encrypted and are considering ways to make it easier to reach friends and families across networks".
Social media giant Facebook bought Instagram and WhatsApp in 2012 and 2014 respectively.
It means that all three apps will support end-to-end encryption, which Instagram now lacks.
To be clear, integrating the three platforms would allow someone who only has a Facebook account to message someone who only has a WhatsApp account or Instagram account, or any combination thereof.
The 1,000-word defence came after Facebook faced intense scrutiny over how it handled data of over two billion users amid several data scandals in recent years.
Facebook plans to integrate WhatsApp and Instagram with its own Messenger service in an attempt to keep users within its ecosystem.
Zuckerberg may get a lot of flack for Facebook's privacy missteps, but as the architect of Facebook's roadmap, it's hard to argue with any of the major moves he's made in the past. When Facebook acquired Instagram and WhatsApp, he promised the companies relative autonomy within Facebook.
Zuckerberg was called to testify in Congress and European Parliament previous year after a scandal that allowed political consultancy group Cambridge Analytica to access the personal information of 87 million users - including Facebook's best guess at their political leanings.
Facebook CEO Mark Zuckerberg published an op-ed in the Wall Street Journal late Thursday to explain his company's business model and address some misconceptions he feels people have about his company.
Instagram's founders, Kevin Systrom and Mike Krieger, left Facebook last autumn. However, this does not tally with the possibility that it may, for example, result in Messenger's ability to see user information from Instagram or vice versa.