The tech giant made changes to the messaging app last month, with only its AI assistant Meta AI able to access it since.
However, the European Commission said that WhatsApp was an "important entry point" for chatbots such as ChatGPTto reach people - and claims that Meta is abusing its power by blocking them.
A Meta spokesperson told the BBC that the EU had "no reason" to intervene in the matter and claimed that it had "incorrectly" assumed WhatsApp Business was an important way for people to use chatbots.
Teresa Ribera, the European Commission's competition chief, said: "We must protect effective competition in this vibrant field, which means we cannot allow dominant tech companies to illegally leverage their dominance to give themselves an unfair advantage."
The EU will wait for Meta's response to their findings and could impose "interim measures" to stop the tech firm from causing "serious and irreparable harm on the market".
Matthias Vermeulen, a director at AWO, a law firm working on EU digital policies, explained that the preliminary findings showed firms operating in the EU could not use their dominance over one market "to unfairly advantage themselves in another".
He explained that while Meta has not been found to have broken the law yet, the company could be forced to reopen WhatsApp to third-party AI assistants should the interim measure be imposed.
Meanwhile, it was recently revealed that Meta will be trialling premium subscriptions for Instagram, Facebook and WhatsApp users in the coming months.
The US tech behemoth's latest experiment with paid services is set to give access to features such as expanded artificial intelligence (AI) capabilities.
However, access to the social media platforms' core services will remain free of charge.
Meta intends to test subscriptions for features such as the Vibes video generation app, which the company says "can bring your ideas to life with new AI visual creation tools".
It is also aiming to use Manus - the Chinese-founded AI firm it agreed to buy in a reported $2billion deal last year - in its subscription plans.
Meta will continue to offer standalone Manus subscriptions to businesses.
