Mr Kohout said the two sides had a "frank" dialogue" in Brussels
The European Union has said it made no headway with Cuba on its human rights record, following talks in Brussels.
The comments were made by Czech Foreign Minister Jan Kohout, who represented the EU at the meeting.
Cuban Foreign Minister Bruno Rodriguez defended Havana's record, saying the common EU position on Cuba - with its focus on human rights - was "obsolete".
The EU lifted sanctions on Cuba in 2008 to encourage democratic reforms, but decided to review the move annually.
"Our views did converge on the issues of climate change and UN reform; they did not in the area of human rights," said Mr Kohout, whose country currently holds the EU presidency.
Raul Castro has introduced a series of reforms since taking office in 2008
"We came back to the issue of political prisoners in Cuba and their health, and the answer we got was that in Cuba there are no political prisoners," the Czech minister added.
However, he described the talks as a "frank" dialogue.
In his turn, Mr Rodriguez said that Havana "is ready to normalise relations, to establish a new start in relationships between the European Union and Cuba".
The Cuban minister urged the 27-member bloc to do away with its common stance on Cuba, saying it was "an obstacle to the process of normalisation" between the two sides.
Mr Rodriguez also stressed that all prisoners in Cuba were afforded full legal rights and a fair trial.
"These are legal decisions, and not a of a political nature. The Cuban penal system fully complies with all standards and domain."
The EU is currently evaluating whether to maintain the full diplomatic ties it restored with the Caribbean island last year or resume the sanctions, which were imposed in 2003 in protest at Havana's imprisonment of more than 70 dissidents.
The sanctions were formally lifted in June 2008 but are subject to a yearly review.
The US has recently eased restrictions on Cuba, allowing Cuban-Americans to visit relatives in Cuba and send money home more easily.
US President Barack Obama said last month Washington was seeking a "new beginning" with Havana.
However, the US maintains its decades-old economic embargo on Cuba.