They said that poor conditions at an overcrowded camp in Moria presented a "serious risk" to at least 3,000 migrants living there.
A man in his 20s said to be a Pakistani was found dead in his tent on Monday.
A 22-year-old Egyptian man and a 46-year-old Syrian man who shared a tent died last week. Reports suggest they inhaled toxic fumes from heaters.
Greek police are now investigating the deaths.
Local media have cited carbon monoxide poisoning as a possible cause of deaths, as the cold winter weather has forced many migrants to use heaters and wood-burning stoves to keep warm.
"Something has got to give," International Rescue Committee Greece director Panos Navrozidis was quoted as saying by Reuters. "We cannot tolerate this wanton loss of life."
The Doctors of the World charity said poor conditions at the camp posed "serious risk" to migrants.
More than 60,000 migrants and refugees - many of them from conflict-ravaged countries like Syria, Iraq and Afghanistan - currently live in camps around Greece.
Aid groups say many of the camps are overcrowded, with Human Rights Watch describing the conditions in some of them as "deplorable and volatile".
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.

The security breach led to the possible theft of bitcoin worth $65m (Â£49m).
Bitfinex told the Reuters news agency on Wednesday that nearly 120,000 bitcoin were stolen from its exchange platform.
All transactions on the virtual exchange have been suspended while the security breach is investigated.
In a statement on its website, Bitfinex said that it was "deeply concerned about the issue and we are committing every resource to try to resolve it".
The hack is one of the biggest thefts in bitcoin's history and is being treated as a "major deal" by many in the virtual currency community.
"Unfortunately, we continue to have vulnerabilities in the form of exchanges and wallets," former Singapore-based bitcoin broker David Moskowitz told the BBC.
"The vulnerabilities almost always occur on the exchange or wallet side and this is an area that continues to need improvement and more secure protocols, no different than when a bank gets robbed."
Securing bitcoin trading platforms has been a key challenge, with hacking and thefts seen as the biggest threats.
In 2014, the Tokyo-based Mt Gox trading exchange declared bankruptcy when hundreds of millions of dollars in bitcoins vanished or were stolen.
But Mr Moskowitz stressed that in spite of the latest alleged theft "the core protocol is extremely robust and has not been hacked".
He said while there would most likely be a price correction in bitcoin, he remained confident that it would continue to be an appealing alternative asset.
Aid groups have raised alarm over the deaths of three migrants on Greece's Lesbos island inside a week.
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The price of bitcoin has fallen more than 10% after the Hong Kong-based digital currency exchange Bitfinex said it had suffered a major hack.