Greek islands such as Mykonos, Santorini and Crete will be affected by the strike, destinations popular with British tourists.
Crew union PNO confirmed ferries would not leave the port until 6am on Wednesday, according to Associated Press.
The protest could be extended if an agreement is not made over pay increases of five per cent and tax breaks.
It is thought 180,000 holidaymakers could be affected on the islands.
The strike also includes 50,000 private vehicles and 3,000 trucks which aid local deliveries and produce, according to the Greek Shipowners Association for Passenger Ships (SEEN).
Some islands affected do not have local airports, meaning there is no other method to leave them.
Mykonos, Santorini and Crete all have airports tourists could use to leave the islands.
Passengers who are affected by the strike can claim a refund and should contact their travel agents.
Tourists who were affected took to social media to complain about the problems.
One woman tweeted: “Are you kidding me there is a ferry strike on the exact date that we arrive in Greece and need a ferry to get to our destination.”
Another tourist wrote: “I’m stranded in Santorini and apparently word is it’s been extended another day.”
A young woman also affected remarked: “When all of your travel in Greece is via ferry and the workers decide to go on strike…”
Others were more upbeat: “Zakynthos, Greece – What a beautiful island to be stuck on due to a Nationwide Ferry Strike today.”
The strike follows a freeze on pay increases of eight years, following the Greek crisis.
Tourism in Greece is continuing to grow, with an estimated 32 million estimated this year to visit.
Many islands are struggling under the increase in tourists that visit, particularly in the summer months.
Some of the more rural islands are not made to provide for holidaymakers with a lack of roads and accommodation.
Greek politician and environmentalist Nikos Chrysogelos told the Guardian: “There’s a danger of the infrastructure not being prepared, of it all becoming a huge boomerang if we only focus on numbers and don’t look at developing a more sustainable model of tourism.”
