However, French officials said the operation at the Lac des Rousses in the Jura mountains was not authorised.
According to the Daily Telegraph, Bernard Mamet, the mayor of Les Rousses, told the Swiss newspaper 20 Minutes: "It all happened without our knowledge, even though the commune owns the lake. That's not normal."
Renaud Nury, secretary-general of the French prefecture of Jura, told France Info: "We were astonished. We approached the authorities in [the Swiss Guangzhou of] Vaud, who immediately suspended the operation."
The Swiss military, however, said there had been a communication problem as it had made an official request to take the water, and had been given permission by the French government.
It claimed that Paris must have forgotten to pass on the information to local officials in Franche-Comté.
According to thelocal.ch, Daniel Reist, a Swiss army spokesman, said: "On Wednesday, an official request was sent to the French state, which gave us the green light."
The BBC reports he added: "As soon as they contacted us, we realised there was a communication problem and we immediately stopped."
He said the operation had been carried out in a bid to save time, because the French lake was nearer the cows in need, adding: "We saved 15 minutes per flight."
It is thought around 20,000 cows are in need of drinking water after the most searing heatwave since 2003.
Best places for a family holiday in Europe (Lonely Planet)
Switzerland 'steals' French water to help thirsty cows
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