In a message, the president said Menderes, who played an important role in the development, improvement, and democratization of Turkey during his term, had been exposed to great oppression following the May 27 coup d’etat.
"Despite the fact that 56 years have passed since his death, Menderes and his colleagues have gradually strengthened their preeminent places in our heart," Erdogan said.
Prime Minister Binali Yildirim also issued a message to mark the death anniversary.
"The deceased Menderes, who sacrificed his life to serve the Turkish nation, was a hero in our hearts," he said.
Menderes was Turkey’s ninth prime minister, who was executed following a bloody coup in 1960, which came to symbolize a dark period in Turkish history.
Menderes was arrested along with all leading Democratic Party (DP) members -- Fatin Rustu Zorlu and Hasan Polatkan -- following the May 27, 1960, military coup. They were accused of violating the constitution as well as embezzling money from state funds and were put on trial by a military court on the island of Yassiada, which is seen as the symbol of the sorrows of Turkish democracy, located in the Sea of Marmara to the southeast of Istanbul.
Following the court's verdict, Menderes was hanged along with Zorlu and Polatkan on the island of Imrali in the Sea of Marmara after a year-long trial.
Menderes had won over 50 percent of the vote in the 1957 general elections before he was jailed and made to stand on trial by a military regime that had overthrown his government.
The 1960 coup paved the way for the military to overthrow governments in 1971, 1980 and 1997.
In 1990, the Turkish government said it regretted the execution of Menderes and his grave in Istanbul was turned into a mausoleum.
Being the last Turkish political leader to be executed after a military coup, Menderes' name today can be found in several public places as a mark of respect.