"Today we are starting to notify people that messages are moving out of the Facebook app and over to the Messenger app," Facebook said in an email response to an AFP inquiry.
"To continue sending messages on mobile, people will need to install the Messenger app."
The change coming in an update to Facebook applications for iPhones and Android-powered mobile devices is starting in "a handful" of countries in Europe.
Messenger was touted as a speedier and superior tool for chats. The switch also lets Facebook focus engineering resources on honing one application instead of dividing resources between two.
Some questioned the wisdom of making Facebook users switch between apps when wanting to engage friends in chats.
Zuckerberg in February cut a $19 billion-deal to takeover free mobile messaging service WhatsApp, saying it is actually worth much more.
The 29-year-old Facebook chief announced the stock and cash purchase, a deal that marries his social network of 1.2 billion active users with WhatsApp's 450 million users.
Facebook users are increasingly linking to the social network with smartphones or tablets.
By the end of 2013, mobile devices accounted for 53 percent of Facebook's advertising revenue, bringing in $1.2 billion in the last quarter and more than $3 billion over the whole year.