It is diplomatically unusual for EU officials to voice an opinion about the candidates for any political role in a member state — especially as the race for the French presidency is not over, with a second round of voting slated for May 6.
The final run-off is between the leader of the Front National party, Marine Le Pen and the centrist Emmanuel Macron who only formed his En Marche party in 2016, having resigned from President Francois Hollande's Socialist party.
Mogherini tweeted her support for Macron in the second round.
Tweet: "See the flags of #France and the #EU fly to welcome the result of @emmanuelmacron, the hope and the future of our generation."
One Twitter user, IT Consultant, Diego Prinawrote: "I think that, in your institutional position, it would be better not to comment on the results of any election in the EU."
Juncker's spokesman Margaritis Schinas tweeted that the Commission president gave his backing to Macron, who is pro-EU.
Tweet: "@JunckerEU congratulated @EmmanuelMacron for his result at the first round and wished him good luck for the rest. #Presidentials2017"
The breach of diplomatic protocol was discussed at a press conference, April 25, when Schinas defended his tweet.
"Really the choice was between defending what Europe represents and another option which aims to destroy Europe. So it's a simple choice and our president therefore thought it would be worthwhile congratulating the candidate who defended the pro-European option," he said.
"There were not many choices. The choice was rather simple, straightforward. Those who defended what Europe stands for, and those who simply want to destroy Europe."
The latest opinion poll for BFM TV shows Macron leading by 64 percent to Le Pen's 36 percent.