Russian soldiers currently patrol between Abkhazian and Georgian forces under a 1994 United Nations ceasefire which allows Moscow to station up to 3,000 soldiers in the region.
It reinforced its peacekeepers this year saying Georgia was preparing to invade, an assertion Tbilisi denies.
"This deployment of Russian railroad forces does not appear to have any legal basis. It is not taking place in the context of the CIS peacekeeping mission, and it is against the express wishes of the Georgian government," de Hoop Scheffer said on Tuesday.
In a statement issued before de Hoop Scheffer spoke, the Russian foreign ministry said that Georgia should stop saying Moscow was bent on annexing Abkhazia.
"It would not be bad if the Georgian side would swap the senseless mantra about the threat of annexation and intervention for practical steps to strengthen ties," the ministry said.
The Kremlin said Dmitry Medvedev, Russia's new president, discussed Moscow's support for Abkhazia with Mikheil Saakashvili, Georgia's president, by telephone on Tuesday.
Javier Solana, the European Union foreign policy chief, is due to travel to Tbilisi this week as part of a joint diplomatic effort with the United States aimed at defusing the tension in the region.