Zapatero, Spain's prime minister between 2004 and 2011, and his foreign minister at the time, Miguel Angel Moratinos, met with Castro on Wednesday during a private visit to the Communist-run island.
The meeting comes as the European Union and Cuba are in talks to try to reset their soured relationship.
"It is an extreme disloyalty with regards to the management of foreign policy," Spanish Foreign Minister Jose Manuel Garcia-Margallo said when asked about the meeting.
"The visit is not only an example of disloyalty, it is an example of inappropriateness," he added.
The Spanish government said it had been informed by Spain's Socialist party that the two would make a private visit to Cuba, but was not aware they would meet with Castro during the trip.
Garcia-Margallo visited Cuba in November but was not invited to meet with Castro as he had wanted.
Since 1996, EU policy toward Cuba has been guided by the so-called Common Position, which rules out full relations with Havana until it makes reforms in areas such as more diverse political participation and freedom of expression.
The EU began lifting some sanctions unilaterally in 2008, the year Fidel Castro retired from the presidency permanently and power passed to his younger brother Raul.
Under Zapatero Spain pushed for the EU to soften its Cuba policy, a position fiercely opposed by Garcia-Margallo's Popular Party.
Spain mediated historic talks between the Cuban government and the Roman Catholic Church that freed 75 political opponents in 2010 and 2011. They had been sentenced to terms ranging from six to 28 years.
Spain is Cuba's third-largest trading partner and the largest European investor in the country, its former colony, according to Spain's foreign ministry.