The Ministry of External Affairs said the development casts a doubt on the Maldivian government's commitment to uphold the rule of law and will raise questions on the credibility of the presidential elections in that country, slated for September.
According to Maldivian media reports, Mr Gayoom, 80, and Chief Justice Abdulla Saeed were handed similar prison terms of one year, seven months and six days by a court which found them guilty of obstructing justice.
In a statement, the MEA said India reiterated its "advice" to the Maldivian government to restore the credibility of the electoral and political process by immediately releasing political prisoners, including Mr Gayoom and the chief justice.
Since the beginning of the political crisis in the Maldives, the ministry said, India has repeatedly urged the Maldivian government to allow all institutions, including its Supreme Court and Parliament, to function in an independent manner and permit genuine political dialogue between all political parties.
"This has also been the demand of the international community at large. It is, therefore, with deep dismay that we learned that the former president of the Maldives as well as the chief justice of the Supreme Court are being sentenced to long prison terms without fair trial," it said in a statement.
"This casts doubt on the commitment of the Government of the Maldives to uphold the rule of law and will also call into question the credibility of the entire process of Presidential elections in September this year," the MEA said.
"It reiterates its advice to the Government of the Maldives to restore the credibility of the electoral and political process by immediately releasing political prisoners including former President Gayoom and Chief Justice Abdulla Saeed and creating the necessary conditions for the participation of all political forces in the Presidential Elections," the ministry said.
Ties between India and Maldives nosedived after Maldivian President Abdulla Yameen declared emergency on February 5, following an order by the Supreme Court to release a group of Opposition leaders who had been convicted in widely-criticised trials.
On February 21, India reacted strongly over the extension of emergency by a month. The emergency was lifted 45 days later.
In February, Maldives declined India's invitation to participate in the eight-day mega naval exercise - Milan - from March 6-13.