Some passengers took to Twitter to complain about a lack of information and refreshments.
One user wrote: "300 passengers stranded at Larnaca, confused messages and no rep in sight. Shocking treatment, no water, nothing."
However, a Thomas Cook spokesperson said the airline had "pulled out all the stops" to ensure passengers were comfortable.
Speaking to the MailOnline, a spokesperson for Thomas Cook Airlines said: "We'd like to sincerely apologise for the delay to this flight. The captain made the decision to return to Larnaca at around 11pm yesterday UK time due to a fault with the air conditioning system.
"Customers would have felt the cabin become much warmer as a result – this is due to the body heat of that many people in an enclosed space.
"Subsequently, we've pulled out all the stops to ensure the customers were taken care of really well. All customers were put up in hotels overnight – mostly in the Hilton – and provided with all meals and drinks."
The spokesperson added that the "departure time from Larnaca will be mid-afternoon UK time" on Thursday.
Best places for a family holiday in Europe (Lonely Planet)
British passengers stranded in Cyprus after Thomas Cook plane aircon fault
Known as the 'garden of England' thanks to its gentle hills and ranging countryside, not to mention its beautiful coastline dotted with sandy beaches including Whitstable and Broadstairs, Kent has been crowned Lonely Planet's best place in Europe for a family holiday. Pictured: the beach at Whitstable in Kent.
Beautiful County Kerry is home to Ireland's iconic rolling green hills and emerald fields. Although it's one of Ireland's most popular tourist spots, there's always a hidden mountain path to get lost on away from the crowds.
This evergreen landscape of valleys, rivers, hills and forests provides activities for everyone to enjoy. Cycling holidays are popular in the area and the Badische Weinstrasse is a 160km-long route that works its way through the foothills of the forest, travelling through the vineyards of the Baden region.
Hungary's beautiful capital is split by the River Danube with a host of wonderful architecture on both sides. Hot springs can be found all over Budapest and offer tourists a unique visitor experience.
Found in the western most part of Austria, Vorarlberg is just by the border with Lichtenstein. Set in the rural hills of the countryside, the region is known for its beautiful architecture.
The Åland archipelago can be a rather confusing area because even though the islands belong to Finland, Swedish is the native language. The archipelago also has its own parliament and has the power to sell products duty free!
It may be known as one of the party capitals of Europe but Ibiza has much more to offer than late nights and loud music. Step off the beaten track and enjoy the island's white beaches, clear waters and secluded sun spots.
Home to the island monastery Mont St-Michel and the Bayeux Tapestry, Normandy has a rich and long history in Europe. The area is known for its rich cuisine and fresh seafood Pictured: Etretat cliff and church
Skomer Island is home to a host of stunning wildlife and it particularly well known for its puffin population. Found off the coast of Pembrokeshire, Skomer is surrounded by beautiful waters and sealife. Marloes Sands has plenty of coastal walks for visitors to enjoy and those in luck may even be able to spot Skomer from the shore.
Bled may be the most famous lake in Slovenia but Lake Bohinj is just as stunning and won't be overcome by crowds in the summer months. Bohinj is the perfect place to indulge in outdoor activities and water sports including kayaking, cycling and climbing. Pictured: Church of St John the Baptist, Bohinj Lake