EU Humanitarian Aid Commissioner Louis Michel said the coup jeopardized cooperation with the EU, "as we are finalizing with the Mauritanian government a 156 million euro program for 2008-2013 to add to assistance already in place".
The EU's executive body, the European Commission, said in a statement that the coup endangered "the exemplary democratic advances which the country has made since the 2005 coup d'etat."
The commission said it would continue to closely watch developments in the country.
A group of renegade army officers staged a coup in the early hours of Wednesday morning, detaining President Sidi Ould Cheikh Abdallahi and Prime Minister Yahya Ould Ahmed Waghf.
The leaders, along with other top government members, were arrested as soldiers were deployed on the streets of the capital and state radio and television was shut down.
Abdallahi became Mauritania's first democratically elected president when a military junta handed power back to a civilian government through elections in 2007 after a bloodless coup in 2005.
The president threatened last month to dissolve parliament after lawmakers filed a motion of no confidence in his new government, which then resigned.
The largely desert country has had a history of coups since its independence from France in 1960.
