A source at the ministry, quoted late Tuesday by Syrian state news agency SANA, described the plan as "a flagrant violation of international law".
The source added that the ministry considered the EU move a bid to "evade international commitments to fund the operation to destroy Syria's chemical weapons," SANA said.
The comments came after a meeting of EU foreign ministers agreed to release frozen funds of Syria's Central Bank and state-owned entities to help pay for the dismantling the country's chemical weapons program.
The Organization for the Prohibition of Chemical Weapons (OPCW) and the UN are participating in a joint mission overseeing the destruction of Syria's chemical weapons program under a UN resolution approved last year.
The OPCW says the cost of destroying chemical materials alone will run between 25 and 30 million euros, but that additional costs are difficult to estimate.
But there are also significant costs associated with the cataloging of the arsenal and verification of its destruction and the deployment of the UN-OPCW mission.
Syria agreed last year to turn over its chemical arsenal after Washington threatened military action in response to a chemical weapons attack outside Damascus in August.
Syria has been gripped by deadly unrest since March 2011. According to reports, the Western powers and their regional allies -- especially Qatar, Saudi Arabia, and Turkey -- support the militants operating inside Syria.
More than 130,000 people have been killed and millions displaced due to the violence.
HH/HH