The Football Association will write to clubs advising players should not use the phrase “from river to the sea” in social media posts as it is “considered offensive to many”.
Critics say the phrase implies the destruction of Israel, but some pro-Palestinian protesters disagree.
The FA also says it will “seek police guidance” if a player uses it again.
Choudhury, 26, posted the phrase, often interpreted as supportive of Palestinian nationalism, on Monday alongside an image of a Palestinian flag.
He later released a statement saying his post had “unfortunately been misinterpreted” and his intention had simply been to “show compassion for the innocent people that are suffering”.
The former England Under-21 international has now deleted the post.
“I share the hope of people around the world that a peaceful resolution can bring an end to the ongoing suffering of innocent people in this conflict,” he added.
Leicester spoke to Choudhury about the matter and shared “concerns that views expressed in this manner – without sufficient context on a deeply nuanced and sensitive topic – are open to misinterpretation, which risks unintentional offence among sections of our communities”.
In a statement on Wednesday, the FA said: “After careful consideration, we will be writing to all clubs to make it clear that this phrase is considered offensive to many, and should not be used by players in social media posts.
“The player has apologised and deleted the tweet. We are strongly encouraging clubs to ensure that players do not post content which may be offensive or inflammatory to any community.
“If this phrase is used again by a football participant, we will seek police guidance on how we should treat it and respond.”
During Saturday’s pro-Palestinian march in London, some people in the crowd chanted the phrase, which refers to land between the River Jordan and the Mediterranean.
Earlier this month, UK home secretary Suella Braverman urged police chiefs to consider interpreting the phrase as an “expression of a violent desire to see Israel erased from the world”.
But that interpretation is disputed by some pro-Palestinian activists who say that most people chanting it are calling for an end to Israel’s occupation of the West Bank and blockade of Gaza, not the destruction of Israel itself.
Prime Minister Rishi Sunak’s spokesman said the phrase is “a deeply offensive chant to many”.
