About 2,500 Indians from China, Japan, Iran and Italy were evacuated earlier.
India has embarked on a "massive" operation involving naval ships and aircraft to bring back some of the hundreds of thousands of nationals stuck abroad due to coronavirus restrictions, the government said.
All incoming international flights were banned in late March as the government imposed one of the world's strictest virus lockdowns, leaving vast numbers of workers and students stranded.
A defence spokesman told AFP on Tuesday that two ships were steaming towards the Maldives and another to the United Arab Emirates -- home to a 3.3-million-strong Indian community, who make up around 30 percent of the Gulf state's population.
A government statement said the evacuations would begin on Thursday and that Indian embassies and high commissions were preparing lists of "distressed Indian citizens".
The consulate in Dubai said that it alone had almost 200,000 applications, appealing on Twitter for "patience and cooperation" as the nation undertakes the "massive task" of repatriation.
The oil-rich Gulf is reliant on the cheap labour of millions of foreigners -- mostly from India, Pakistan, Nepal and Sri Lanka -- many of whom live in squalid camps far from the region's showy skyscrapers and malls.
But coronavirus and the devastating economic impact of the pandemic has left many workers sick and others unemployed, unpaid and at the mercy of sometimes unscrupulous employers.
The UAE has been the most vocal among Gulf countries in demanding governments take workers back, with almost 23,000 having left as of April 20.
But New Delhi had until now refused to cooperate, balking at the logistical and safety nightmare of repatriating and quarantining millions of returning citizens.
About 2,500 Indians from China, Japan, Iran and Italy were evacuated by the government before banning international and domestic travel.