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 BBC.
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.
Mr Muizzu's (centre) victory last October was seen as a setback for India
"It is for them to decide where they go and how they go about their international relations," Indian Foreign Ministry Spokesperson Randhir Jaiswal said last week in response to questions on Mr Muizzu's visit to Beijing.
He also said there was no update on the withdrawal of Indian troops from the Maldives. India says its security personnel are in the Maldives to maintain three maritime rescue and surveillance aircraft it had donated to the country.
The Indian Ocean archipelago has long been under India's sphere of influence and Mr Muizzu wants to change that.
In December, the Maldivian government said it was terminating a bilateral agreement with India that permitted Delhi to collaborate in mapping the seabed in Maldivian territorial waters.
A Maldivian government spokesman said the deal, set to expire in June next year, would not be renewed.
Soon after he won the elections in October last year, Mr Muizzu told the BBC he would review all the bilateral agreements signed with India by the previous administration of Mr Solih, who had adopted an India First policy.
Delhi and Beijing are competing for a foothold in the strategically located islands.