"It's not the first time that the president makes such discriminatory remarks, that's why we decided to fine him," Istvan Haller, a spokesperson for the Council told AFP.
The presidency did not immediately react to the decision.
In 2010, during a visit to Slovenia, Basescu alleged that "many nomadic Roma live from what they steal".
Over 30 human rights organisations slammed the president's comments as "racist" and Roma rights group Romani Criss lodged a complaint.
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"The fine is low but it sends a clear message: even if you are president, when you make discriminatory comments you will get a sanction", he added.
Basescu had already received two warnings from the CNCD anti-discrimination council over anti-Roma remarks: in 2007, after calling a journalist a "dirty Gypsy" and in 2011 for accusing Roma of "stealing" in buses.
Romania counts the largest Roma minority in Europe, estimated at about two million people according to NGOs, 620,000 according to a census.
Last December, the founder of France's far-right National Front, Jean-Marie Le Pen, was fined 5,000 euros (USD 6,800) for accusing Roma of stealing "naturally".