"Zapatero [Spain's prime minister] has ignored all opposition requests to respect human rights," he said. Moratinos "came to ensure Spain's investments in Cuba".
Felipe Perez Roque, the Cuban foreign minister, said the talks had not touched on the subject of Cuban political prisoners.
"This is not a matter we discuss with other countries," he said, and he said that Moratinos had not brought it up.
Perez Roque agreed to talks with Spain, he adamantly opposed discussions with the rest of Europe until it lifted EU sanctions "definitively."
"We cannot talk with anyone imposing sanctions on us," he said.
Spain's policy on Cuba shifted after Jose Luis Rodriguez Zapatero, the socialist prime minister, came to power in 2004.
His conservative predecessor, Jose Maria Aznar, had adopted a policy of isolating Cuba.
On Tuesday, Moratinos also met Raul Castro, Cuba's interim president since July, when his brother, Fidel, underwent intestinal surgery.
The European Union imposed political and diplomatic sanctions on Cuba in 2003 after the government arrested and sentenced 75 dissidents to jail terms of six to 28 years.
Sixteen have since been released due to poor health.
The EU must decide in June whether to extend the sanctions.