Obama reportedly told Zapatero that he understood that not everything could be changed overnight, but that Cuba should realise that now is the time to make changes.
"Have [Moratinos] tell the Cuban authorities we understand that change can't happen overnight, but down the road, when we look back at this time, it should be clear that now is when those changes began," Obama told Zapatero, according to diplomatic sources quoted by El Pais.
"We're taking steps, but if they don't take steps too, it's going to be very hard for us to continue."
The US and Cuba have had no diplomatic relations for almost 50 years.
|Obama lifted restrictions on travels and remittances to Cuba earlier this year [EPA]
Obama signalled a thawing of ties with Cuba when he removed limits on Cuban-Americans travelling and sending remittances to the island.
He also started talks on migration issues and the resumption of direct mail services broken off in 1963 between the two countries which are just 145km apart.
He has however said that the 47-year-old US trade embargo against Cuba, the main point of contention between the two countries, should stay in place until Cuba releases political prisoners and improves human rights.
Spain, one of Cuba's biggest trading partners, has highlighted improved ties between the European Union and Cuba as one of its priorities when it takes over the rotating EU presidency in January.