Kovind, who arrived in the island on Thursday, was received by Diaz-Canel with military honors at the Palace of the Revolution before they held talks in private.
According to an official release, both leaders agreed to continue developing "solidarity and friendly relations" and vowed to boost cooperation for the well-being of their nations.
Diaz-Canel and Kovind expressed particular interest in boosting economic cooperation and investments as well as collaboration in science and technology and renewable energy, according to the release.
Kovind and Diaz-Canel also witnessed the signing of three new cooperation agreements in the areas of biotechnology and healthcare.
At the ceremony, the health ministries of Cuba and India inked a memorandum of understanding (MOU) to increase cooperation in traditional medicine and homeopathy.
Meanwhile, envoys from the ministries of science and technology agreed on an MOU to deepen collaboration on biotechnology.
In this context, a letter of intent was signed between BioCubaFarma, the island's state company for pharmaceutical and biotechnology products, with India's Kalam Institute of Health Technology.
Earlier, Kovind paid tribute to the island's national hero, Jose Marti, by laying a flower wreath at Havana's Revolution Square. He also visited Cuba's main biotechnology research center to learn about innovative drugs to fight lung and skin cancer as well as foot ulcers caused by diabetes.
Cuba and India have historic ties which date back to 1959 when famous guerrilla fighter Ernesto 'Che' Guevara visited New Delhi. Along with Cuba, India was also a founding member of the Non-Aligned Movement.