The officials had responded to a social media post from Mr Modi, calling him a “clown”, “terrorist” and a “puppet of Israel”.
A foreign ministry spokesperson said the comments were personal and did not represent the views of the government.
Male’s response came after the remarks set off an uproar on Indian social media.
“All government officials responsible for the comments have been suspended from their posts effective immediately”, a spokesperson for President Mohamed Muizzu’s office told the RTV
There is already tension between India and the island nation after Mr Muizzu asked a contingent of about 75 Indian troops to leave the country after he came to power last year.
The three suspended ministers are Malsha Shareef, Mariyam Shiuna and Abdulla Mahzoom Majid.
Despite strong calls for their sacking, Maldivian media noted the three officials have been only suspended.
The trio made the controversial comments in response to Mr Modi’s post on X (formerly Twitter) which included photos promoting tourism to the Indian island chain of Lakshadweep.
Ms Shiuna also compared India with cow dung.
This sparked outrage on Indian social media and got hashtags such as #BoycottMaldives and #ExploreIndianIslands trending.
Some said they would cancel their holidays to the Maldives – Indians were among the largest group of tourists who visited the Maldives last year. The CEO of Indian ticket-booking site EaseMyTrip said his company had suspended all flight bookings to the Maldives.
The archipelago is famous for its silver sand beaches, resorts and coral islands.
Prominent Indians, including bollywood star akshay kumar as well as some cricketers, expressed dismay at the comments.
Former Maldivian president Ibrahim Mohamed Solih strongly condemned what he termed as “hateful language against India” by the three officials.
“India has always been a good friend to Maldives, and we must not allow such callous remarks to negatively impact the age-old friendship between our two countries”, he said on X.
Another former president Mohamed Nasheed called the language in the social media posts “appalling”.
The controversial posts were deleted following the uproar.
The controversy also comes ahead of Mr Muizzu making a five-day state visit to India’s rival China beginning Monday.
Mr Muizzu’s trip to Beijing is considered a high-profile snub to India as previous Maldivian leaders first visited India after being elected. He chose Turkey as his first international port of call after he took over in November.
This will be seen as a diplomatic setback for Delhi, which is trying to match China’s growing footprint in the Indian Ocean region.
