Russia is demanding that the Swiss pay storage charges for two trains carrying aid destined for Georgia that has been blocked at customs posts since last year.
The Swiss defence ministry said on Tuesday that Bern was also being told to pay charges for having described the cargo incorrectly.
The payment demand goes against a deal agreed earlier this month by the Russian foreign minister, Igor Ivanov, during a meeting in Bern with his Swiss counterpart, Joseph Deiss.
Russian authorities stopped the trains on the grounds that their contents ran the risk of falling into the hands of rebels in the breakaway republic of Chechnya, with which Georgia shares a land border.
The trains are full of second hand army supplies and Switzerland has said it wants to get the shipments back. Moscow, however, says it will not release the trains until the charges are paid.
One train is being held at the Russian-Ukrainian border. The other is stuck at Russia's border with Azerbaijan.
The Swiss foreign ministry said the goods consisted of 50 off-road vehicles, 27 tonnes of military clothing, medical items, x-ray machines and cooking equipment.
It said there were no weapons, weapon parts or combat clothing included in the load.
The goods were intended for use by Georgia's border police and prison service. However, Russian authorities stopped the trains because they disagreed with the Swiss government's declaration of the items as "diplomatic goods".
swissinfo with agencies