President Nicolas Maduro presented an altered version during his weekly television show on Sunday.
"My music is for everyone to listen to and enjoy, not to be used as propaganda that intends to manipulate the will of a people who are screaming for their liberty and a better future", Fonsi said in a message posted to Instagram.
"That you illegally appropriate a song [Despacito] doesn't compare with the crime you commit and have committed in Venezuela".
Parts of the lyrics were changed to promote the plans for the constituent assembly, which has been heavily criticized by world leaders.
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But the song's lyrics, which talk about love and romance on the beaches of Puerto Rico is considered too risque for authorities in Malaysia. Meanwhile, clashes between the government and protesters against the so-called "constituent assembly" have turned extremely violent, with at least 100 people dead in the fighting as of last week.
"Despacito", which means "very slowly" in Spanish, is a song very popular since its release in January.
Maduro has also applauded the creative group, who reworked on the song and asked the audience what they thought about it, the BBC reported.
Anti-government demonstrations started in the country in early April after the Supreme Court annulled the opposition-dominated National Assembly and removed lawmakers' immunity. Those in favor of rewriting the constitution, however, say the president is simply hoping to restore peace in his fractured country. He has said that only the new constitution will help Venezuela out of its economic and political crisis. During the 2016 USA presidential election, artists such as the Rolling Stones, Aerosmith and Adele slammed Donald Trump for playing their music at campaign events, while Queen famously ordered the NY real estate mogul to stop using "We Are the Champions" during his appearances.