In a speech to businessmen in the northeastern city of Fortaleza on Thursday, Guedes complained about the media coverage of the Bolsonaro administration, arguing that they prefer to report on the President's comments rather than the country's progress.
"What I see in the newspapers is that he insulted (French First Lady Michelle) Bachelet, or that he called (French President Emmanuel) Macron's wife ugly.
"He did say that and it's true - the woman is indeed ugly," he said, prompting laughter in the audience.
"There's no such thing as an ugly woman, there's only women seen from the wrong angle," the Minister added.
Guedes later apologized for what he called a "joke" involving Brigitte Macron, media reports said.
"The Minister's intention was to show that relevant and urgent issues for the country don't receive the space they deserve in the public debate," read his statement to the press.
"There was no intention to express personal offences."
The incident came amid the spat between Macron and Bolsanero over Brazil's treatment of the fires burning in the Amazon. Macron recently threatened to scrap the trade deal agreed between the European Union and Mercosur, the South American customs union, unless Brazil did more to preserve the Amazon rainforest.
Responding to the French President, Bolsonaro had said that the notion of prioritizing the matter was "reminiscent of (a) colonial mindset (that was) inappropriate in the 21st century".
The conflict between the two Presidents got more personal after Bolsonaro cancelled a meeting in Brasilia with the French Foreign Minister at the last minute.
Later, on the eve of August's G-7 summit, Macron tweeted his concern about the Amazon fires and called for an international response, prompting an angry reaction from the Brazilian President, who posted a sarcastic comment on a social media post mocking Brigitte Macron's physical appearance.
Macron called the comment "extraordinarily disrespectful to my wife" and added that he hoped the Brazilian people would soon have a President worthy of them.
( With inputs from IANS )